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Liu X, Jin W, Bao D, He T, Wang W, Li Z, Yang X, Tong Y, Shu M, Wang Y, Yuan J, Yang Y. DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data. Comput Struct Biotechnol J 2024; 23:2057-2066. [PMID: 38783901 PMCID: PMC11112131 DOI: 10.1016/j.csbj.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Intronic polyadenylation (IPA) refers to a particular type of alternative polyadenylation where a gene makes use of a polyadenylation site located within its introns. Aberrant IPA events have been observed in various types of cancer. IPA can produce noncoding transcripts or truncated protein-coding transcripts with altered coding sequences in the resulting protein product. Therefore, IPA events hold the potential to act as a reservoir of tumor neoantigens. Here, we developed a computational method termed DIPAN, which incorporates IPA detection, protein fragmentation, and MHC binding prediction to predict IPA-derived neoantigens. Utilizing RNA-seq from breast cancer cell lines and ovarian cancer clinical samples, we demonstrated the significant contribution of IPA events to the neoantigen repertoire. Through mass spectrometry immunopeptidome analysis, we further illustrated the processing and presentation of IPA-derived neoantigens on the surface of cancer cells. While most IPA-derived neoantigens are sample-specific, shared neoantigens were identified in both cancer cell lines and clinical samples. Furthermore, we demonstrated an association between IPA-derived neoantigen burden and overall survival in cancer patients.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Dengyi Bao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tongxin He
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wenhui Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Tong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meng Shu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Li Y, Li W, Fan B, Zhang Y, Li Z, Lin K, Huang K, Yang Z, Ma S, Sun H. A novel mutation alters GNE bifunctional enzyme activity and leads to familial inherited GNE diseases. Gene 2024; 927:148750. [PMID: 38971548 DOI: 10.1016/j.gene.2024.148750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/19/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Distal myopathies are a group of rare heterogeneous diseases that are mostly caused by genetic factors. At least 20 genes have been associated with distal myopathies. We performed whole-exome sequencing to identify the genetic cause of disease in a family with distal myopathy. Following the American College of Medical Genetics and Genomics (ACMG) guidelines, we analyzed the sequencing results and screened suspicious mutations based on mutation frequency, functional impact, and disease inheritance pattern. The harmfulness of the mutations was predicted using bioinformatics methods, and the pathogenic mutations were determined. We identified a novel amino acid mutation (NP_005467.1:p.S663L) on the GNE gene that may cause familial distal myopathy. This mutation is the result of the simultaneous mutation of two adjacent nucleotides (c.1988C > T, c.1989C > A) in the codon. First, we measured the mRNA and protein expression of the GNE gene in the lymphoblastoid cell lines (LCLs) of the probands and their family members. Second, GNE vectors carrying the novel mutation, two other known pathogenic mutations, and the wild-type gene were constructed and transfected into HEK293T cells. The enzymatic activity of these GNE variants was investigated and showed that the p.S663L mutation significantly reduced the activity of the bifunctional GNE enzyme without altering the expression level of the GNE protein. Furthermore, the mutation may also alter the immunogenicity of the 3' end of the GNE protein, potentially affecting its oligomer formation. In this study, a novel GNE gene mutation that may cause distal myopathy was identified, expanding the spectrum of genetic mutations associated with this disease.
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Affiliation(s)
- Yufei Li
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Wenwu Li
- Department of Neurology, People's Hospital of Chuxiong Yi Autonomous Prefecture, Yunnan 675000, China
| | - Baitong Fan
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Yao Zhang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Zhaoqing Li
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China; School of Life Sciences, Yunnan University, Kunming, Yunnan 650504, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Kai Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Shaohui Ma
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China
| | - Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, China.
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Walt HK, Ahn SJ, Hoffmann FG. Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion. Mol Phylogenet Evol 2024; 198:108134. [PMID: 38901473 DOI: 10.1016/j.ympev.2024.108134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/28/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.
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Affiliation(s)
- Hunter K Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Seung-Joon Ahn
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biotechnology and Biocomputing, Mississippi State University, Mississippi State, MS 39762, USA.
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Yuan Y, Duan W, Yang N, Sun C, Nie Q, Li J, Lian L. Transcriptome analysis of long non-coding RNA associated with embryonic muscle development in chickens. Br Poult Sci 2024; 65:394-402. [PMID: 38738875 DOI: 10.1080/00071668.2024.2335935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
1. Skeletal muscle is an important component of chicken carcass. In chickens, the number of muscle fibres is fixed during the embryonic period, and muscle development during the embryonic period determines the muscle development potential after hatching.2. Beijing-You (BY) and Cornish (CN) chickens show completely different growth rates and body types, and two breeds were used in this study to explore the role of lncRNAs in muscle development during different chicken embryonic periods. A systematic analysis of lncRNAs and mRNAs were conducted in the pectoral muscle tissues of BY and CN chickens at embryonic days 11 (ED11), 13 (ED13), 15 (ED15), 17 (ED17), and 1-day-old (D1) using RNA-seq. A total of 4,104 differentially expressed transcripts (DETs) were identified among the five stages, including 2,359 lncRNAs and 1,745 mRNAs.3. The number of DETs between the two breeds at ED17 (1,658 lncRNAs and 1,016 mRNAs) was much higher than the total number of DET at all the other stages (692 lncRNAs and 729 mRNAs), indicating that the two breeds show the largest difference in gene regulation at ED17.4. Correlation analysis was performed for all differentially expressed lncRNAs and mRNAs during the five periods. Forty-three, cis interaction pairs of lncRNA-mRNA related to chicken muscle development were predicted. The expression of four pairs was verified, and the results showed MSTRG.12395.2-FGFBP2 and MSTRG.18590.6-FMOD were significantly up-regulated in CN at ED11 compared to BY and might be important candidate genes for embryonic muscle development.
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Affiliation(s)
- Y Yuan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - W Duan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - N Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - C Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Q Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - J Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - L Lian
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Bharadwaj R, Nath P, Phukan JK, Deb K, Gogoi V, Bhattacharyya DK, Barah P. Integrative ceRNA network analysis identifies unique and shared molecular signatures in Bipolar Disorder and Schizophrenia. J Psychiatr Res 2024; 176:47-57. [PMID: 38843579 DOI: 10.1016/j.jpsychires.2024.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/28/2024] [Accepted: 05/29/2024] [Indexed: 07/29/2024]
Abstract
Bipolar Disorder (BPD) and Schizophrenia (SCZ) are complex psychiatric disorders with shared symptomatology and genetic risk factors. Understanding the molecular mechanisms underlying these disorders is crucial for refining diagnostic criteria and guiding targeted treatments. In this study, publicly available RNA-seq data from post-mortem samples of the basal ganglia's striatum were analyzed using an integrative computational approach to identify differentially expressed (DE) transcripts associated with SCZ and BPD. The analysis aimed to reveal both shared and distinct genes and long non-coding RNAs (lncRNAs) and to construct competitive endogenous RNA (ceRNA) networks within the striatum. Furthermore, the functional implications of these identified transcripts are explored, alongside their presence in established databases such as BipEx and SCHEMA. A significant outcome of our analysis was the identification of 21 DEmRNAs and 1 DElncRNA shared between BPD and SCZ across the Caudate, Putamen, and Nucleus Accumbens. Another noteworthy finding was the identification of Hub nodes within the ceRNA networks that were linked to major psychosis. Particularly, MED19, HNRNPC, MAGED4B, KDM5A, GOLGA7, CHASERR, hsa-miR-4778-3p, hsa-miR-4739, and hsa-miR-4685-5p emerged as potential biomarkers. These findings shed light on the common and unique molecular signatures underlying BPD and SCZ, offering significant potential for the advancement of diagnostic and therapeutic strategies tailored to these psychiatric disorders.
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Affiliation(s)
- Rachayita Bharadwaj
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, 784028, Assam, India
| | - Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, 784028, Assam, India
| | - Jadab Kishore Phukan
- Department of Biochemistry, Lokopriya Gopinath Bordoloi Regional Institute of Mental Health (LGBRIMH), Sonitpur, Tezpur, 784001, Assam, India
| | - Kunal Deb
- Department of Psychiatry, Lokopriya Gopinath Bordoloi Regional Institute of Mental Health (LGBRIMH), Sonitpur, Tezpur, 784001, Assam, India
| | - Vijay Gogoi
- Department of Psychiatry, Lokopriya Gopinath Bordoloi Regional Institute of Mental Health (LGBRIMH), Sonitpur, Tezpur, 784001, Assam, India
| | - Dhruba Kumar Bhattacharyya
- Department of Computer Science and Engineering, Tezpur University, Napaam, Sonitpur, 784028, Assam, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, 784028, Assam, India.
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Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N, Robledo D. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biol 2024; 22:160. [PMID: 39075472 DOI: 10.1186/s12915-024-01952-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. RESULTS We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. CONCLUSIONS Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
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Affiliation(s)
- S J Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - R Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - S J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - J E Bron
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - P R Villamayor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - O Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - M D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - R D Houston
- Benchmark Genetics, 1 Pioneer BuildingMilton Bridge, Edinburgh TechnopolePenicuik, UK
| | - N Robinson
- Nofima AS, Tromsø, Norway.
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), Deakin University, Melbourne, VIC, 3225, Australia.
| | - D Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain.
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Gjerga E, Dewenter M, Britto-Borges T, Grosso J, Stein F, Eschenbach J, Rettel M, Backs J, Dieterich C. Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms. Database (Oxford) 2024; 2024:baae060. [PMID: 39051433 PMCID: PMC11270014 DOI: 10.1093/database/baae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/03/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
Time-course multi-omics data of a murine model of progressive heart failure (HF) induced by transverse aortic constriction (TAC) provide insights into the molecular mechanisms that are causatively involved in contractile failure and structural cardiac remodelling. We employ Illumina-based transcriptomics, Nanopore sequencing and mass spectrometry-based proteomics on samples from the left ventricle (LV) and right ventricle (RV, RNA only) of the heart at 1, 7, 21 and 56 days following TAC and Sham surgery. Here, we present Transverse Aortic COnstriction Multi-omics Analysis (TACOMA), as an interactive web application that integrates and visualizes transcriptomics and proteomics data collected in a TAC time-course experiment. TACOMA enables users to visualize the expression profile of known and novel genes and protein products thereof. Importantly, we capture alternative splicing events by assessing differential transcript and exon usage as well. Co-expression-based clustering algorithms and functional enrichment analysis revealed overrepresented annotations of biological processes and molecular functions at the protein and gene levels. To enhance data integration, TACOMA synchronizes transcriptomics and proteomics profiles, enabling cross-omics comparisons. With TACOMA (https://shiny.dieterichlab.org/app/tacoma), we offer a rich web-based resource to uncover molecular events and biological processes implicated in contractile failure and cardiac hypertrophy. For example, we highlight: (i) changes in metabolic genes and proteins in the time course of hypertrophic growth and contractile impairment; (ii) identification of RNA splicing changes in the expression of Tpm2 isoforms between RV and LV; and (iii) novel transcripts and genes likely contributing to the pathogenesis of HF. We plan to extend these data with additional environmental and genetic models of HF to decipher common and distinct molecular changes in heart diseases of different aetiologies. Database URL: https://shiny.dieterichlab.org/app/tacoma.
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Affiliation(s)
- Enio Gjerga
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Matthias Dewenter
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
- Institute of Experimental Cardiology, Medical Faculty Heidelberg, Heidelberg University, INF 669, Heidelberg 69120, Germany
- Internal Medicine VIII, Heidelberg University Hospital, INF 669, Heidelberg 69120, Germany
| | - Thiago Britto-Borges
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Johannes Grosso
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
- Institute of Experimental Cardiology, Medical Faculty Heidelberg, Heidelberg University, INF 669, Heidelberg 69120, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
- Proteomics Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Jessica Eschenbach
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Johannes Backs
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
- Institute of Experimental Cardiology, Medical Faculty Heidelberg, Heidelberg University, INF 669, Heidelberg 69120, Germany
- Internal Medicine VIII, Heidelberg University Hospital, INF 669, Heidelberg 69120, Germany
- Helmholtz Institute for Translational AngioCardioScience (HI-TAC), MDC at Heidelberg University, Heidelberg 69120, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, INF 669, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK)—Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
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8
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Garg P, Vanamamalai VK, Sharma S. In-silico analysis of cattle blood transcriptome to identify lncRNAs and their role during bovine tuberculosis. Sci Rep 2024; 14:16537. [PMID: 39019929 PMCID: PMC11255290 DOI: 10.1038/s41598-024-67001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nucleotides that do not code for functional proteins. Although, genes play a vital role in immune response against a disease, it is less known that lncRNAs also contribute through gene regulation. Bovine tuberculosis is a significant zoonotic disease caused by Mycobacterium bovis (M. bovis) in cattle. Here, we report the in-silico analysis of the publicly available transcriptomic data of calves infected with M. bovis. A total of 51,812 lncRNAs were extracted across all the samples. A total of 216 genes and 260 lncRNAs were found to be differentially expressed across all the 4 conditions-infected vs uninfected at 8- and 20-week post-infection (WPI), 8 vs 20-WPI of both infected and uninfected. Gene Ontology and Functional annotation showed that 8 DEGs were annotated with immune system GOs and 2 DEGs with REACTOME immune system pathways. Co-expression analysis of DElncRNAs with DEGs revealed the involvement of lncRNAs with the genes annotated with Immune related GOs and pathways. Overall, our study sheds light on the dynamic transcriptomic changes in response to M. bovis infection, particularly highlighting the involvement of lncRNAs with immune-related genes. The identified immune pathways and gene-lncRNA interactions offer valuable insights for further research in understanding host-pathogen interactions and potential avenues for genetic improvement strategies in cattle.
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Affiliation(s)
- Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad, Telangana, 500032, India.
- Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, Faridabad Rd, Faridabad, Haryana, 121001, India.
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9
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Zhong J, Zhang J, Zhang Y, Ge Y, He W, Liang C, Gao Y, Zhu Z, Machado RAR, Zhou W. Heat stress reprograms herbivory-induced defense responses in potato plants. BMC PLANT BIOLOGY 2024; 24:677. [PMID: 39014327 PMCID: PMC11253553 DOI: 10.1186/s12870-024-05404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
Climate change is predicted to increase the occurrence of extreme weather events such as heatwaves, which may thereby impact the outcome of plant-herbivore interactions. While elevated temperature is known to directly affect herbivore growth, it remains largely unclear if it indirectly influences herbivore performance by affecting the host plant they feed on. In this study, we investigated how transient exposure to high temperature influences plant herbivory-induced defenses at the transcript and metabolic level. To this end, we studied the interaction between potato (Solanum tuberosum) plants and the larvae of the potato tuber moth (Phthorimaea operculella) under different temperature regimes. We found that P. operculella larvae grew heavier on leaves co-stressed by high temperature and insect herbivory than on leaves pre-stressed by herbivory alone. We also observed that high temperature treatments altered phylotranscriptomic patterns upon herbivory, which changed from an evolutionary hourglass pattern, in which transcriptomic responses at early and late time points after elicitation are more variable than the ones in the middle, to a vase pattern. Specifically, transcripts of many herbivory-induced genes in the early and late defense stage were suppressed by HT treatment, whereas those in the intermediate stage peaked earlier. Additionally, we observed that high temperature impaired the induction of jasmonates and defense compounds upon herbivory. Moreover, using jasmonate-reduced (JA-reduced, irAOC) and -elevated (JA-Ile-elevated, irCYP94B3s) potato plants, we showed that high temperature suppresses JA signaling mediated plant-induced defense to herbivore attack. Thus, our study provides evidences on how temperature reprograms plant-induced defense to herbivores.
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Affiliation(s)
- Jian Zhong
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Jinyi Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yadong Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yang Ge
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengjuan Liang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchatel, Neuchatel, 2000, Switzerland
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
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10
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Sigeman H, Downing PA, Zhang H, Hansson B. The rate of W chromosome degeneration across multiple avian neo-sex chromosomes. Sci Rep 2024; 14:16548. [PMID: 39020011 PMCID: PMC11255319 DOI: 10.1038/s41598-024-66470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1-4.5 million years (Myr). We show that the translocated regions have maintained 68.3-97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.
| | - Philip A Downing
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Hongkai Zhang
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
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11
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Camarena ME, Theunissen P, Ruiz M, Ruiz-Orera J, Calvo-Serra B, Castelo R, Castro C, Sarobe P, Fortes P, Perera-Bel J, Albà MM. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. SCIENCE ADVANCES 2024; 10:eadn3628. [PMID: 38985879 PMCID: PMC11235171 DOI: 10.1126/sciadv.adn3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source of tumor-specific antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling and immunopeptidomics data. Combining human leukocyte antigen-epitope binding predictions and experimental validation experiments, we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs, including two peptides that can trigger an immune response in humanized mice. We identify a subset of 33 tumor-specific long noncoding RNAs expressing novel cancer antigens shared by more than 10% of the HCC samples analyzed, which, when combined, cover a large proportion of the patients. The results of the study open avenues for extending the range of anticancer vaccines.
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Affiliation(s)
| | - Patrick Theunissen
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Marta Ruiz
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Beatriz Calvo-Serra
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Castelo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carla Castro
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Pablo Sarobe
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | | | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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12
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. Am J Hum Genet 2024; 111:1282-1300. [PMID: 38834072 PMCID: PMC11267525 DOI: 10.1016/j.ajhg.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
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Affiliation(s)
- Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Pagé C Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christopher A Jin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Matthew T Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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13
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Dehasque M, Morales HE, Díez-Del-Molino D, Pečnerová P, Chacón-Duque JC, Kanellidou F, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Nikolskiy P, Danilov GK, Giannì M, van der Sluis L, Higham T, Heintzman PD, Oskolkov N, Gilbert MTP, Götherström A, van der Valk T, Vartanyan S, Dalén L. Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell 2024; 187:3531-3540.e13. [PMID: 38942016 DOI: 10.1016/j.cell.2024.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/08/2024] [Accepted: 05/17/2024] [Indexed: 06/30/2024]
Abstract
A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Héloïse Muller
- Master de Biologie, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon I, Universite de Lyon, 69007 Lyon, France
| | - Valerii Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Albert Protopopov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 3 University Embankment, Box 199034, Saint-Petersburg, Russia
| | - Maddalena Giannì
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Laura van der Sluis
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Peter D Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; SciLifeLab, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
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14
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Zhang J, Shi Y, Yang Y, Oakeshott JG, Wu Y. Differentiation in detoxification gene complements, including neofunctionalization of duplicated cytochrome P450 genes, between lineages of cotton bollworm, Helicoverpa armigera. Mol Ecol 2024:e17463. [PMID: 38984610 DOI: 10.1111/mec.17463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Here we investigate the evolutionary dynamics of five enzyme superfamilies (CYPs, GSTs, UGTs, CCEs and ABCs) involved in detoxification in Helicoverpa armigera. The reference assembly for an African isolate of the major lineages, H. a. armigera, has 373 genes in the five superfamilies. Most of its CYPs, GSTs, UGTs and CCEs and a few of its ABCs occur in blocks and most of the clustered genes are in subfamilies specifically implicated in detoxification. Most of the genes have orthologues in the reference genome for the Oceania lineage, H. a. conferta. However, clustered orthologues and subfamilies specifically implicated in detoxification show greater sequence divergence and less constraint on non-synonymous differences between the two assemblies than do other members of the five superfamilies. Two duplicated CYPs, which were found in the H. a. armigera but not H. a. conferta reference genome, were also missing in 16 Chinese populations spanning two different lineages of H. a. armigera. The enzyme produced by one of these duplicates has higher activity against esfenvalerate than a previously described chimeric CYP mutant conferring pyrethroid resistance. Various transposable elements were found in the introns of most detoxification genes, generating diverse gene structures. Extensive resequencing data for the Chinese H. a. armigera and H. a. conferta lineages also revealed complex copy number polymorphisms in 17 CCE001s in a cluster also implicated in pyrethroid metabolism, with substantial haplotype differences between all three lineages. Our results suggest that cotton bollworm has a versatile complement of detoxification genes which are evolving in diverse ways across its range.
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Affiliation(s)
- Jianpeng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Yu Shi
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - John G Oakeshott
- Applied Biosciences, Macquarie University, Sydney, New South Wales, Australia
| | - Yidong Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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15
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Haese-Hill W, Crouch K, Otto TD. Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic Acids Res 2024; 52:W39-W44. [PMID: 38752499 PMCID: PMC11223846 DOI: 10.1093/nar/gkae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/06/2024] [Accepted: 04/30/2024] [Indexed: 07/06/2024] Open
Abstract
As sequencing genomes has become increasingly popular, the need for annotation of the resulting assemblies is growing. Structural and functional annotation is still challenging as it includes finding the correct gene sequences, annotating other elements such as RNA and being able to submit those data to databases to share it with the community. Compared to de novo assembly where contiguous chromosomes are a sign of high quality, it is difficult to visualize and assess the quality of annotation. We developed the Companion web server to allow non-experts to annotate their genome using a reference-based method, enabling them to assess the output before submitting to public databases. In this update paper, we describe how we have included novel methods for gene finding and made the Companion server more efficient for annotation of genomes of up to 1 Gb in size. The reference set was increased to include genomes of interest for human and animal health from the fungi and arthropod kingdoms. We show that Companion outperforms existing comparable tools where closely related references are available.
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Affiliation(s)
| | - Kathryn Crouch
- School of Infection & Immunity, University of Glasgow, UK
| | - Thomas D Otto
- School of Infection & Immunity, University of Glasgow, UK
- LPHI, CNRS, INSERM, Université de Montpellier, France
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16
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Johnston MJ, Lee JJY, Hu B, Nikolic A, Hasheminasabgorji E, Baguette A, Paik S, Chen H, Kumar S, Chen CCL, Jessa S, Balin P, Fong V, Zwaig M, Michealraj KA, Chen X, Zhang Y, Varadharajan S, Billon P, Juretic N, Daniels C, Rao AN, Giannini C, Thompson EM, Garami M, Hauser P, Pocza T, Ra YS, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska W, Perek-Polnik M, Agnihotri S, Mack S, Ellezam B, Weil A, Rich J, Bourque G, Chan JA, Yong VW, Lupien M, Ragoussis J, Kleinman C, Majewski J, Blanchette M, Jabado N, Taylor MD, Gallo M. TULIPs decorate the three-dimensional genome of PFA ependymoma. Cell 2024:S0092-8674(24)00697-4. [PMID: 38986619 DOI: 10.1016/j.cell.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/26/2022] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Posterior fossa group A (PFA) ependymoma is a lethal brain cancer diagnosed in infants and young children. The lack of driver events in the PFA linear genome led us to search its 3D genome for characteristic features. Here, we reconstructed 3D genomes from diverse childhood tumor types and uncovered a global topology in PFA that is highly reminiscent of stem and progenitor cells in a variety of human tissues. A remarkable feature exclusively present in PFA are type B ultra long-range interactions in PFAs (TULIPs), regions separated by great distances along the linear genome that interact with each other in the 3D nuclear space with surprising strength. TULIPs occur in all PFA samples and recur at predictable genomic coordinates, and their formation is induced by expression of EZHIP. The universality of TULIPs across PFA samples suggests a conservation of molecular principles that could be exploited therapeutically.
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Affiliation(s)
- Michael J Johnston
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ana Nikolic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Elham Hasheminasabgorji
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada
| | - Seungil Paik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Haifen Chen
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Sachin Kumar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Selin Jessa
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Vernon Fong
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Melissa Zwaig
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | | | - Xun Chen
- Department of Anatomy and Cell Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Yanlin Zhang
- School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada
| | - Srinidhi Varadharajan
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pierre Billon
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nikoleta Juretic
- Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Caterina Giannini
- Pediatric Hematology-Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Miklos Garami
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Peter Hauser
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Timea Pocza
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Young Shin Ra
- Department of Neurosurgery, University of Ulsan, Asan Medical Center, Seoul 05505, South Korea
| | - Byung-Kyu Cho
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Kyu-Chang Wang
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Ji Yeoun Lee
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Wieslawa Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, University of Warsaw, 04-730 Warsaw, Poland
| | - Marta Perek-Polnik
- Department of Oncology, The Children's Memorial Health Institute, University of Warsaw, 04-730 Warsaw, Poland
| | - Sameer Agnihotri
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, United States of America
| | - Stephen Mack
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Alex Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Jeremy Rich
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Jennifer A Chan
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - V Wee Yong
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Claudia Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Mathieu Blanchette
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada; School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H3A 3J1, Canada.
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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17
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Xu D, Feng H, Li Y, Pan J, Yao Z. Molecular mechanisms of neutron radiation dose effects on M 1 generation peas. Appl Radiat Isot 2024; 212:111423. [PMID: 38981165 DOI: 10.1016/j.apradiso.2024.111423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/08/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
The dose effect of radiation has long been a topic of concern, but the molecular mechanism behind it is still unclear. In this study, dried pea seeds were irradiated with 252Cf fission neutron source. Through analyzing the transcriptome and proteome of M1 generation pea (Pisum sativum L.) leaves, we studied the molecular rule and mechanism of neutron dose effect. Our results showed three important rules of global gene expression in the studied dose range. The rule closely related to the neutron absorbed dose at the transcription and translation levels is: the greater the difference in neutron absorbed dose between two radiation treatment groups, the greater the difference in differential expression between the two groups and the control group. We also obtained important sensitive metabolic pathways of neutron radiation, as well as related key genes. Furthermore, the overall molecular regulation mechanism of dose effect was revealed based on the main functional items obtained. Our research results can be applied to appropriate radiation dose estimation and agricultural production practice.
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Affiliation(s)
- Dapeng Xu
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000, China; Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China.
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yafeng Li
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000, China; Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Ze'en Yao
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000, China; Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
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18
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Morales-Vicente DA, Tahira AC, Woellner-Santos D, Amaral MS, Berzoti-Coelho MG, Verjovski-Almeida S. The Human Developing Cerebral Cortex Is Characterized by an Elevated De Novo Expression of Long Noncoding RNAs in Excitatory Neurons. Mol Biol Evol 2024; 41:msae123. [PMID: 38913688 PMCID: PMC11221658 DOI: 10.1093/molbev/msae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
The outstanding human cognitive capacities are computed in the cerebral cortex, a mammalian-specific brain region and the place of massive biological innovation. Long noncoding RNAs have emerged as gene regulatory elements with higher evolutionary turnover than mRNAs. The many long noncoding RNAs identified in neural tissues make them candidates for molecular sources of cerebral cortex evolution and disease. Here, we characterized the genomic and cellular shifts that occurred during the evolution of the long noncoding RNA repertoire expressed in the developing cerebral cortex and explored putative roles for these long noncoding RNAs in the evolution of the human brain. Using transcriptomics and comparative genomics, we comprehensively annotated the cortical transcriptomes of humans, rhesus macaques, mice, and chickens and classified human cortical long noncoding RNAs into evolutionary groups as a function of their predicted minimal ages. Long noncoding RNA evolutionary groups showed differences in expression levels, splicing efficiencies, transposable element contents, genomic distributions, and transcription factor binding to their promoters. Furthermore, older long noncoding RNAs showed preferential expression in germinative zones, outer radial glial cells, and cortical inhibitory (GABAergic) neurons. In comparison, younger long noncoding RNAs showed preferential expression in cortical excitatory (glutamatergic) neurons, were enriched in primate and human-specific gene co-expression modules, and were dysregulated in neurodevelopmental disorders. These results suggest different evolutionary routes for older and younger cortical long noncoding RNAs, highlighting old long noncoding RNAs as a possible source of molecular evolution of conserved developmental programs; conversely, we propose that the de novo expression of primate- and human-specific young long noncoding RNAs is a putative source of molecular evolution and dysfunction of cortical excitatory neurons, warranting further investigation.
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Affiliation(s)
- David A Morales-Vicente
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Daisy Woellner-Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Maria G Berzoti-Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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19
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Huang A, Feng S, Ye Z, Zhang T, Chen S, Chen C, Chen S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1828. [PMID: 38999668 PMCID: PMC11243878 DOI: 10.3390/plants13131828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Luffa spp. is an important worldwide cultivated vegetable and medicinal plant from the Cucurbitaceae family. In this study, we report a high-quality chromosome-level genome of the high-generation inbred line SG261 of Luffa acutangula. The genomic sequence was determined by PacBio long reads, Hi-C sequencing reads, and 10× Genomics sequencing, with an assembly size of 739.82 Mb, contig N50 of 18.38 Mb, and scaffold N50 of 56.08 Mb. The genome of L. acutangula SG261 was predicted to contain 27,312 protein-coding genes and 72.56% repetitive sequences, of which long terminal repeats (LTRs) were an important form of repetitive sequences, accounting for 67.84% of the genome. Phylogenetic analysis reveals that L. acutangula evolved later than Luffa cylindrica, and Luffa is closely related to Momodica charantia. Comparing the genome of L. acutangula SG261 and L. cylindrica with PacBio data, 67,128 high-quality structural variations (SVs) and 55,978 presence-absence variations (PAVs) were identified in SG261, resulting in 2424 and 1094 genes with variation in the CDS region, respectively, and there are 287 identical genes affected by two different structural variation analyses. In addition, we found that the transcription factor FY (FLOWERING LOCUS Y) families had a large expansion in L. acutangula SG261 (flowering in the morning) compared to L. cylindrica (flowering in the afternoon), which may result in the early flowering time in L. acutangula SG261. This study provides valuable reference for the breeding of and pan-genome research into Luffa species.
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Affiliation(s)
- Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
| | - Shuo Feng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Zhuole Ye
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shenglong Chen
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shijun Chen
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
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20
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Markee A, Godfrey RK, Frandsen PB, Weng YM, Triant DA, Kawahara AY. De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes. Genome Biol Evol 2024; 16:evae148. [PMID: 38957923 PMCID: PMC11258402 DOI: 10.1093/gbe/evae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues.
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Affiliation(s)
- Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Yi-Ming Weng
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Deborah A Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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21
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Wang D, Jin Y, Guan C, Yang Q, He G, Xu N, Han X. Evolutionary divergence of CXE gene family in green plants unveils that PtoCXEs overexpression reduces fungal colonization in transgenic Populus. TREE PHYSIOLOGY 2024; 44:tpae071. [PMID: 38905297 DOI: 10.1093/treephys/tpae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/23/2024]
Abstract
Plant enzymes significantly contribute to the rapidly diversified metabolic repertoire since the colonization of land by plants. Carboxylesterase is just one of the ubiquitous, multifunctional and ancient enzymes that has particularly diversified during plant evolution. This study provided a status on the carboxylesterase landscape within Viridiplantae. A total of 784 carboxylesterases were identified from the genome of 31 plant species representing nine major lineages of sequenced Viridiplantae and divided into five clades based on phylogenetic analysis. Clade I carboxylesterase genes may be of bacterial origin and then expanded and diversified during plant evolution. Clade II was first gained in the ancestor of bryophytes after colonization of land by plants, Clade III and Clade IV in ferns which were considered the most advanced seedless vascular plants, while Clade V was gained in seed plants. To date, the functions of carboxylesterase genes in woody plants remain unclear. In this study, 51 carboxylesterase genes were identified from the genome of Populus trichocarpa and further divided into eight classes. Tandem and segmental duplication events both contributed to the expansion of carboxylesterase genes in Populus. Although carboxylesterase genes were proven to enhance resistance to pathogens in many herbaceous species, relevant researches on forest trees are still needed. In this study, pathogen incubation assays showed that overexpressing of six Class VI carboxylesterases in Populus tomentosa, to a greater or lesser degree, reduced colonization of detached leaves by fungus Cytospora chrysosperma. A significant difference was also found in functional divergence patterns for genes derived from different gene duplication events. Functional differentiation of duplicated carboxylesterase genes in Populus was proved for the first time by in vivo physiological analysis. The identification of the potentially anti-fungal PtoCXE06 gene also laid a theoretical foundation for promoting the genetic improvement of disease-resistance traits in forest trees.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1 Dong Xiaofu, Haidian District, Beijing 100091, China
| | - Yuting Jin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghuadonglu, Haidian District, Beijing 100083, China
| | - Chaonan Guan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghuadonglu, Haidian District, Beijing 100083, China
| | - Qi Yang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, No. 666 Wusu street, Lin'an district, Hangzhou 311300, China
| | - Gang He
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, No. 2025 Chengluo Avenue, Longquanyi District, Chengdu 610106, China
| | - Nan Xu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghuadonglu, Haidian District, Beijing 100083, China
| | - Xuemin Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1 Dong Xiaofu, Haidian District, Beijing 100091, China
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22
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Tang AD, Felton C, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Detecting haplotype-specific transcript variation in long reads with FLAIR2. Genome Biol 2024; 25:173. [PMID: 38956576 PMCID: PMC11218413 DOI: 10.1186/s13059-024-03301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, the use of short-read RNA-seq has limited the community's ability to interrogate both forms of RNA variation simultaneously. RESULTS We employ long-read sequencing technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We develop a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generate nanopore data with high sequence accuracy from H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We apply our workflow to identify key inosine isoform associations to help clarify the prominence of ADAR in tumorigenesis. CONCLUSIONS Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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Affiliation(s)
- Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Roger Volden
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, USA.
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23
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Yang T, Cai Y, Huang T, Yang D, Yang X, Yin X, Zhang C, Yang Y, Yang Y. A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance. HORTICULTURE RESEARCH 2024; 11:uhae119. [PMID: 38966866 PMCID: PMC11220182 DOI: 10.1093/hr/uhae119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 04/14/2024] [Indexed: 07/06/2024]
Abstract
Avocado (Persea americana Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the relatively high unsaturated fatty acid content, provides significant health benefits. We herein present a telomere-to-telomere gapless genome assembly (841.6 Mb) of West Indian avocado. The genome contains 40 629 predicted protein-coding genes. Repeat sequences account for 57.9% of the genome. Notably, all telomeres, centromeres, and a nucleolar organizing region are included in this genome. Fragments from these three regions were observed via fluorescence in situ hybridization. We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes. These genes, which are typically clustered on chromosomes, may be derived from gene duplication events. Five NLR genes (Pa11g0262, Pa02g4855, Pa07g3139, Pa07g0383, and Pa02g3196) were highly expressed in leaves, stems, and fruits, indicating they may be involved in avocado disease responses in multiple tissues. We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves, stems, and fruits. Pa02g0113, which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruits. These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.
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Affiliation(s)
- Tianyu Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Cai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Tianping Huang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Gardening & Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Danni Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xingyu Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yin
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunqiang Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yongping Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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24
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
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Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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Szrajer S, Gray D, Ylla G. The genome assembly and annotation of the cricket Gryllus longicercus. Sci Data 2024; 11:708. [PMID: 38942791 PMCID: PMC11213874 DOI: 10.1038/s41597-024-03554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
The order Orthoptera includes insects such as grasshoppers, katydids, and crickets, among which there are important species for ecosystem stability and pollination, as well as research organisms in different fields such as neurobiology, ecology, and evolution. Crickets, with more than 2,400 described species, are emerging as novel model research organisms, for their diversity, worldwide distribution, regeneration capacity, and their characteristic acoustic communication. Here we report the assembly and annotation of the first New World cricket, that of Gryllus longicercus Weissman & Gray 2019. The genome assembly, generated by combining 44.54 Gb of long reads from PacBio and 120.44 Gb of short Illumina reads, has a length of 1.85 Gb. The genome annotation yielded 19,715 transcripts from 14,789 gene models.
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Affiliation(s)
- Szymon Szrajer
- Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, 30-387, Poland
| | - David Gray
- Department of Biology, California State University Northridge, Northridge, CA, 91330-8303, USA.
| | - Guillem Ylla
- Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, 30-387, Poland.
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Shi Q, Zhang Q, Shao M. Accurate assembly of multiple RNA-seq samples with Aletsch. Bioinformatics 2024; 40:i307-i317. [PMID: 38940157 PMCID: PMC11211816 DOI: 10.1093/bioinformatics/btae215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION High-throughput RNA sequencing has become indispensable for decoding gene activities, yet the challenge of reconstructing full-length transcripts persists. Traditional single-sample assemblers frequently produce fragmented transcripts, especially in single-cell RNA-seq data. While algorithms designed for assembling multiple samples exist, they encounter various limitations. RESULTS We present Aletsch, a new assembler for multiple bulk or single-cell RNA-seq samples. Aletsch incorporates several algorithmic innovations, including a "bridging" system that can effectively integrate multiple samples to restore missed junctions in individual samples, and a new graph-decomposition algorithm that leverages "supporting" information across multiple samples to guide the decomposition of complex vertices. A standout feature of Aletsch is its application of a random forest model with 50 well-designed features for scoring transcripts. We demonstrate its robust adaptability across different chromosomes, datasets, and species. Our experiments, conducted on RNA-seq data from several protocols, firmly demonstrate Aletsch's significant outperformance over existing meta-assemblers. As an example, when measured with the partial area under the precision-recall curve (pAUC, constrained by precision), Aletsch surpasses the leading assemblers TransMeta by 22.9%-62.1% and PsiCLASS by 23.0%-175.5% on human datasets. AVAILABILITY AND IMPLEMENTATION Aletsch is freely available at https://github.com/Shao-Group/aletsch. Scripts that reproduce the experimental results of this manuscript is available at https://github.com/Shao-Group/aletsch-test.
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Affiliation(s)
- Qian Shi
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, United States
| | - Qimin Zhang
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, United States
| | - Mingfu Shao
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, United States
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Li S, Tan X, He Z, Jiang L, Li Y, Yang L, Hoffmann AA, Zhao C, Fang J, Ji R. Transcriptome-wide N 6-methyladenosine profiling reveals growth-defense trade-offs in the response of rice to brown planthopper (Nilaparvata lugens) infestation. PEST MANAGEMENT SCIENCE 2024. [PMID: 39031631 DOI: 10.1002/ps.8265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 07/22/2024]
Abstract
BACKGROUND N6-Methyladenosine (m6A) is a common messenger RNA (mRNA) modification that affects various physiological processes in stress responses. However, the role of m6A modifications in plants responses to herbivore stress remains unclear. RESULTS Here, we found that an infestation of brown planthopper (Nilaparvata lugens) female adults enhanced the resistance of rice to N. lugens. The m6A methylome analysis of N. lugens-infested and uninfested rice samples was performed to explore the interaction between rice and N. lugens. The m6A methylation mainly occurred in genes that were actively expressed in rice following N. lugens infestation, while an analysis of the whole-genomic mRNA distribution of m6A showed that N. lugens infestation caused an overall decrease in the number of m6A methylation sites across the chromosomes. The m6A methylation of genes involved in the m6A modification machinery and several defense-related phytohormones (jasmonic acid and salicylic acid) pathways was increased in N. lugens-infested rice compared to that in uninfested rice. In contrast, m6A modification levels of growth-related phytohormone (auxin and gibberellin) biosynthesis-related genes were significantly attenuated during N. lugens infestation, accompanied by the down-regulated expression of these transcripts, indicating that rice growth was restricted during N. lugens attack to rapidly optimize resource allocation for plant defense. Integrative analysis of the differential patterns of m6A methylation and the corresponding transcripts showed a positive correlation between m6A methylation and transcriptional regulation. CONCLUSION The m6A modification is an important strategy for regulating the expression of genes involved in rice defense and growth during rice-N. lugens interactions. These findings provide new ideas for formulating strategies to control herbivorous pests. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xinyang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yali Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Liu Yang
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Australia
| | - Chunqing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jichao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui, China
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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Li L, Zhang L, Luo L, Shen F, Zhao Y, Wu H, Huang Y, Hou R, Yue B, Zhang X. Adaptive Expression and ncRNA Regulation of Genes Related to Digestion and Metabolism in Stomach of Red Pandas during Suckling and Adult Periods. Animals (Basel) 2024; 14:1795. [PMID: 38929414 PMCID: PMC11200446 DOI: 10.3390/ani14121795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Red pandas evolved from carnivores to herbivores and are unique within Carnivora. Red pandas and carnivorous mammals consume milk during the suckling period, while they consume bamboo and meat during the adult period, respectively. Red pandas and carnivorous mammal ferrets have a close phylogenetic relationship. To further investigate the molecular mechanisms of dietary changes and nutrient utilization in red pandas from suckling to adult, comparative analysis of the whole transcriptome was performed on stomach tissues from red pandas and ferrets during the suckling and adult periods. The main results are as follows: (1) we identified ncRNAs for the first time in stomach tissues of both species, and found significant expression changes of 109 lncRNAs and 106 miRNAs in red pandas and 756 lncRNAs and 109 miRNAs in ferrets between the two periods; (2) up-regulated genes related to amino acid transport regulated by lncRNA-miRNA-mRNA networks may efficiently utilize limited bamboo amino acids in adult red pandas, while up-regulated genes related to amino acid degradation regulated by lncRNAs may maintain the balance of amino acid metabolism due to larger daily intakes in adult ferrets; and (3) some up-regulated genes related to lipid digestion may contribute to the utilization of rich nutrients in milk for the rapid growth and development of suckling red pandas, while up-regulated genes associated with linoleic acid metabolism regulated by lncRNA-miRNA-mRNA networks may promote cholesterol decomposition to reduce health risks for carnivorous adult ferrets. Collectively, our study offers evidence of gene expression adaptation and ncRNA regulation in response to specific dietary changes and nutrient utilization in red pandas during suckling and adult periods.
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Affiliation(s)
- Lu Li
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Lijun Luo
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Yanni Zhao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China; (H.W.); (Y.H.)
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China; (H.W.); (Y.H.)
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
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Li Q, Chao T, Wang Y, Xuan R, Guo Y, He P, Zhang L, Wang J. Transcriptome analysis revealed the characteristics and functions of long non-coding RNAs in the hypothalamus during sexual maturation in goats. Front Vet Sci 2024; 11:1404681. [PMID: 38938911 PMCID: PMC11210318 DOI: 10.3389/fvets.2024.1404681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
The hypothalamus is an essential neuroendocrine area in animals that regulates sexual development. Long non-coding RNAs (lncRNAs) are hypothesized to regulate physiological processes related to animal reproduction. However, the regulatory mechanism by which lncRNAs participate in sexual maturity in goats is poorly known, particularly from birth to sexual maturation. In this study, RNAseq analysis was conducted on the hypothalamus of four developmental stages (1day (D1, n = 5), 2 months (M2, n = 5), 4 months (M4, n = 5), and 6 months (M6, n = 5)) of Jining grey goats. The results showed that a total of 237 differentially expressed lncRNAs (DELs) were identified in the hypothalamus. Among these, 221 DELs exhibited cis-regulatory effects on 693 target genes, while 24 DELs demonstrated trans-regulatory effects on 63 target genes. The target genes of these DELs are mainly involved in biological processes related to energy metabolism, signal transduction and hormone secretion, such as sphingolipid signaling pathway, adipocytokine signaling pathway, neurotrophic signaling pathway, glutamatergic synapse, P53 signaling pathway and GnRH signaling pathway. In addition, XR_001918477.1, TCONS_00077463, XR_001918760.1, and TCONS_00029048 and their potential target genes may play a crucial role in the process of goat sexual maturation. This study advances our understanding of lncRNA in hypothalamic tissue during sexual maturation in goats and will give a theoretical foundation for improving goat reproductive features.
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Affiliation(s)
- Qing Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Yanyan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Yanfei Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Peipei He
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Lu Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai’an, China
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Grigorev K, Nelson TM, Overbey EG, Houerbi N, Kim J, Najjar D, Damle N, Afshin EE, Ryon KA, Thierry-Mieg J, Thierry-Mieg D, Melnick AM, Mateus J, Mason CE. Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses. Nat Commun 2024; 15:4950. [PMID: 38862496 PMCID: PMC11166648 DOI: 10.1038/s41467-024-48929-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
The advent of civilian spaceflight challenges scientists to precisely describe the effects of spaceflight on human physiology, particularly at the molecular and cellular level. Newer, nanopore-based sequencing technologies can quantitatively map changes in chemical structure and expression at single molecule resolution across entire isoforms. We perform long-read, direct RNA nanopore sequencing, as well as Ultima high-coverage RNA-sequencing, of whole blood sampled longitudinally from four SpaceX Inspiration4 astronauts at seven timepoints, spanning pre-flight, day of return, and post-flight recovery. We report key genetic pathways, including changes in erythrocyte regulation, stress induction, and immune changes affected by spaceflight. We also present the first m6A methylation profiles for a human space mission, suggesting a significant spike in m6A levels immediately post-flight. These data and results represent the first longitudinal long-read RNA profiles and RNA modification maps for each gene for astronauts, improving our understanding of the human transcriptome's dynamic response to spaceflight.
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Affiliation(s)
- Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Theodore M Nelson
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Center for STEM, University of Austin, Austin, TX, USA
- BioAstra, Inc, New York, NY, USA
| | - Nadia Houerbi
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Deena Najjar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information (NCBI), National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information (NCBI), National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Jaime Mateus
- Space Exploration Technologies Corporation (SpaceX), Hawthorne, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, New York, NY, USA.
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Li S, Tan XY, He Z, Shen C, Li YL, Qin L, Zhao CQ, Luo GH, Fang JC, Ji R. The dynamics of N 6-methyladenine RNA modification in resistant and susceptible rice varieties responding to rice stem borer damage. INSECT SCIENCE 2024. [PMID: 38831720 DOI: 10.1111/1744-7917.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent modification in cellular RNA which orchestrates diverse physiological and pathological processes during stress response. However, the differential m6A modifications that cope with herbivore stress in resistant and susceptible crop varieties remain unclear. Here, we found that rice stem borer (RSB) larvae grew better on indica rice (e.g., MH63, IR64, Nanjing 11) than on japonica rice varieties (e.g., Nipponbare, Zhonghua 11, Xiushui 11). Then, transcriptome-wide m6A profiling of representative resistant (Nipponbare) and susceptible (MH63) rice varieties were performed using a nanopore direct RNA sequencing approach, to reveal variety-specific m6A modifications against RSB. Upon RSB infestation, m6A methylation occurred in actively expressed genes in Nipponbare and MH63, but the number of methylation sites decreased across rice chromosomes. Integrative analysis showed that m6A methylation levels were closely associated with transcriptional regulation. Genes involved in herbivorous resistance related to mitogen-activated protein kinase, jasmonic acid (JA), and terpenoid biosynthesis pathways, as well as JA-mediated trypsin protease inhibitors, were heavily methylated by m6A, and their expression was more pronounced in RSB-infested Nipponbare than in RSB-infested MH63, which may have contributed to RSB resistance in Nipponbare. Therefore, dynamics of m6A modifications act as the main regulatory strategy for expression of genes involved in plant-insect interactions, which is attributed to differential responses of resistant and susceptible rice varieties to RSB infestation. These findings could contribute to developing molecular breeding strategies for controlling herbivorous pests.
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Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xin-Yang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chen Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ya-Li Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Lang Qin
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chun-Qing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Wuhu, Anhui Province, China
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34
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Klčová B, Balarynová J, Trněný O, Krejčí P, Cechová MZ, Leonova T, Gorbach D, Frolova N, Kysil E, Orlova A, Ihling С, Frolov A, Bednář P, Smýkal P. Domestication has altered gene expression and secondary metabolites in pea seed coat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2269-2295. [PMID: 38578789 DOI: 10.1111/tpj.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/09/2024] [Indexed: 04/07/2024]
Abstract
The mature seed in legumes consists of an embryo and seed coat. In contrast to knowledge about the embryo, we know relatively little about the seed coat. We analyzed the gene expression during seed development using a panel of cultivated and wild pea genotypes. Gene co-expression analysis identified gene modules related to seed development, dormancy, and domestication. Oxidoreductase genes were found to be important components of developmental and domestication processes. Proteomic and metabolomic analysis revealed that domestication favored proteins involved in photosynthesis and protein metabolism at the expense of seed defense. Seed coats of wild peas were rich in cell wall-bound metabolites and the protective compounds predominated in their seed coats. Altogether, we have shown that domestication altered pea seed development and modified (mostly reduced) the transcripts along with the protein and metabolite composition of the seed coat, especially the content of the compounds involved in defense. We investigated dynamic profiles of selected identified phenolic and flavonoid metabolites across seed development. These compounds usually deteriorated the palatability and processing of the seeds. Our findings further provide resources to study secondary metabolism and strategies for improving the quality of legume seeds which comprise an important part of the human protein diet.
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Affiliation(s)
- Barbora Klčová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Jana Balarynová
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
| | - Oldřich Trněný
- Agricultural Research Ltd., Zemědělská 1, Troubsko, 664 41, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Monika Zajacová Cechová
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Daria Gorbach
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Nadezhda Frolova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Elana Kysil
- Department of Bioorganic Chemistry, Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, Halle (Saale), 06120, Germany
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Сhristian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle (Saale), 06120, Germany
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry, Timiryazev Institute of Plant Physiology, Botanicheskaja 36, Moscow, 127276, Russia
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Sciences, Palacky University, 17. listopadu 1192/12, Olomouc, 771 46, Czech Republic
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Šlechtitelů 27, Olomouc, 773 71, Czech Republic
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35
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Zhu S, Yuan S, Niu R, Zhou Y, Wang Z, Xu G. RNAirport: a deep neural network-based database characterizing representative gene models in plants. J Genet Genomics 2024; 51:652-664. [PMID: 38518981 DOI: 10.1016/j.jgg.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/24/2024]
Abstract
A 5'-leader, known initially as the 5'-untranslated region, contains multiple isoforms due to alternative splicing (aS) and alternative transcription start site (aTSS). Therefore, a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation efficiency. Here, we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant species. We rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-leader. To further assign a representative 5'-end, we train the deep-learning model 5'leaderP to learn aTSS-mediated 5'-end distribution patterns from cap-analysis gene expression data. The model accurately predicts the 5'-end, confirmed experimentally in Arabidopsis and rice. The representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport (http://www.rnairport.com/leader5P/). The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation, identical to the project recently initiated by human GENCODE.
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Affiliation(s)
- Sitao Zhu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Yulu Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Zhao Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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36
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Vargas A, DeBiasse M, Dykes L, Edgar A, Hayes T, Groso D, Babonis L, Martindale M, Ryan J. Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore. NAR Genom Bioinform 2024; 6:lqae072. [PMID: 38895105 PMCID: PMC11184263 DOI: 10.1093/nargab/lqae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.
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Affiliation(s)
- Alexandra M Vargas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, Radford University, Radford, VA 24142, USA
| | - Lana L Dykes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Daniel J Groso
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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37
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Hockens C, Lorenzi H, Wang TT, Lei EP, Rosin LF. Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species. PLoS Genet 2024; 20:e1011329. [PMID: 38913752 PMCID: PMC11226059 DOI: 10.1371/journal.pgen.1011329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 07/05/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the center of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments co-orienting these separated kinetochores. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology.
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Affiliation(s)
- Clio Hockens
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hernan Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tricia T. Wang
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leah F. Rosin
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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38
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Zhao F, Huang Z, He B, Liu K, Li J, Liu Z, Lin G. Comparative genomics of two Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis: With emphasis on antithrombotic genes and their corresponding proteins. Int J Biol Macromol 2024; 270:132278. [PMID: 38750856 DOI: 10.1016/j.ijbiomac.2024.132278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Leeches secrete various biologically active substances which have important medical and pharmaceutical values in antithrombotic treatments. Here, we provide a high quality genome of two Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis, based on which, we identified 22 antithrombotic gene families, including fourteen coagulation inhibitors, four platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. The total numbers of antithrombotic genes were similar between H. nipponia (N = 86) and H. tianjinensis (N = 83). Molecular evolution analysis showed that no significant differences were detected between the two species in any of the three selection indices (dN, dS, and dN/dS), nor in the number of sites under positive/purifying selection. RNA-Seq based gene expression analysis showed that the overall expression patterns of the antithrombotic gene families were not significantly deviated between the two species. Our results indicated that there were rather close similarities between the two leeches on genomic characteristics, especially for the molecular evolution and expression of antithrombotic genes. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from the two Asian medicinal leeches to date. These results will greatly facilitate the research and application of leech derivatives for medical and pharmaceutical purposes of thrombosis.
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Affiliation(s)
- Fang Zhao
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Bo He
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China
| | - Kaiqing Liu
- Engineering Research Center for Exploitation and Utilization of Leech Resources in Universities of Yunnan Province, School of Agronomy and Life Sciences, Kunming University, Kunming 650214, China
| | - Junyu Li
- Department of Ultrasonography, People's Hospital of Fengdu County, Chongqing City, Fengdu 408200, China
| | - Zichao Liu
- Engineering Research Center for Exploitation and Utilization of Leech Resources in Universities of Yunnan Province, School of Agronomy and Life Sciences, Kunming University, Kunming 650214, China; Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji'an 343009, China.
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39
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Li W, Cao Z, Xu F, Zhang X, Sun Y, Xie Z, Ning C, Zhang Q, Wang D, Tang H. Whole transcriptome sequencing reveals key genes and ceRNA regulatory networks associated with pimpled eggs in hens. Poult Sci 2024; 103:103715. [PMID: 38652954 PMCID: PMC11063507 DOI: 10.1016/j.psj.2024.103715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Eggshell is one of the most important indicators of egg quality, and due to low shell strength, pimple eggs (PE) are more susceptible to breakage, thus causing huge economic losses to the egg industry. At the current time, the molecular mechanisms that regulate the formation of pimple eggs are poorly understood. In this study, uterine tissues of PE-laying hens (n = 8) and normal egg (NE) -laying hens (n = 8) were analyzed by whole transcriptome sequencing, and a total of 619 differentially expressed mRNAs (DE mRNAs), 122 differentially expressed lncRNAs (DE lncRNAs) and 21 differentially expressed miRNAs (DE miRNAs) were obtained. Based on the targeting relationship among DE mRNAs, DE lncRNAs and DE miRNAs, we constructed a competitive endogenous RNA (ceRNA) network including 12 DE miRNAs, 19 DE lncRNAs, and 128 DE mRNAs. Considering the large amount of information contained in the network, we constructed a smaller ceRNA network to better understand the complex mechanisms of pimple egg formation. The smaller ceRNA network network contains 7 DE lncRNAs (LOC107056551, LOC121109367, LOC121108909, LOC121108862, LOC112530033, LOC121113165, LOC107054145), 5 DE miRNAs (gga-miR-6568-3p, gga-miR-31-5p, gga-miR-18b-3p, gga-miR-1759-3p, gga-miR-12240-3p) and 7 DE mRNAs (CABP1, DNAJC5, HCN3, HPCA, IBSP, KCNT1, OTOP3), and these differentially expressed genes may play key regulatory roles in the formation of pimpled eggs in hens. This study provides the overall expression profiles of mRNAs, lncRNAs and miRNAs in the uterine tissues of hens, which provides a theoretical basis for further research on the molecular mechanisms of pimpled egg formation, and has potential applications in improving eggshell quality.
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Affiliation(s)
- Wenqiang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Zhi Cao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Fei Xu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Xuguang Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Yifei Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Zhongbiao Xie
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science & Technology, Shandong Agricultural University, Taian City, Shandong Province, 271018, China.
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Wang X, Guo S, Xiong L, Wu X, Bao P, Kang Y, Cao M, Ding Z, Liang C, Pei J, Guo X. Complete characterization of the yak testicular development using accurate full-length transcriptome sequencing. Int J Biol Macromol 2024; 271:132400. [PMID: 38759851 DOI: 10.1016/j.ijbiomac.2024.132400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Alternative splicing is a prevalent phenomenon in testicular tissues. Due to the low assembly accuracy of short-read RNA sequencing technology in analyzing post-transcriptional regulatory events, full-length (FL) transcript sequencing is highly demanded to accurately determine FL splicing variants. In this study, we performed FL transcriptome sequencing of testicular tissues from 0.5, 1.5, 2.5, and 4-year-old yaks and 4-year-old cattle-yaks using Oxford Nanopore Technologies. The obtained sequencing data were predicted to have 47,185 open reading frames (ORFs), including 26,630 complete ORFs, detected 7645 fusion transcripts, 15,355 alternative splicing events, 25,798 simple sequence repeats, 7628 transcription factors, and 35,503 long non-coding RNAs. A total of 40,038 novel transcripts were obtained from the sequencing data, and the proportion was almost close to the number of known transcripts identified. Structural analysis and functional annotation of these novel transcripts resulted in the successful annotation of 9568 transcripts, with the highest and lowest annotation numbers in the Nr and KOG databases, respectively. Weighted gene co-expression network analysis revealed the key regulatory pathways and hub genes at various stages of yak testicular development. Our findings enhance our comprehension of transcriptome complexity, contribute to genome annotation refinement, and provide foundational data for further investigations into male sterility in cattle-yaks.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Lin Xiong
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Yandong Kang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Mengli Cao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Jie Pei
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
| | - Xian Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024; 17:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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Varela-Martínez E, Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. The landscape of long noncoding RNA expression in the goat brain. J Dairy Sci 2024; 107:4075-4091. [PMID: 38278299 DOI: 10.3168/jds.2023-23966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024]
Abstract
The brain regulates multiple metabolic processes, such as food intake, energy expenditure, insulin secretion, hepatic glucose production, and glucose and fatty acid metabolism in adipose tissue, which are fundamental for the maintenance of energy and glucose homeostasis during lactation and pregnancy. In addition, brain expression has a fundamental impact on the development of maternal behavior. Although brain functions are partly regulated by long noncoding RNAs (lncRNAs), their expression profiles have not been characterized in depth in any ruminant species. We have sequenced the transcriptome of 12 brain tissues from 3 goats that were 1 mo pregnant and 4 nonpregnant goats to investigate their lncRNA expression patterns. Between 4,363 (adenohypophysis) and 4,604 (olfactory bulb) lncRNAs were expressed in brain tissues, leading us to establish a set of 794 already annotated lncRNAs and 5,098 novel lncRNA candidates. The detected lncRNAs shared features with those of other mammals, and tissue-specific lncRNAs were enriched in brain development-related terms. Differential expression analyses between goats that were 1 mo pregnant and nonpregnant goats showed that the lncRNA expression profiles of certain brain regions experience substantial changes associated with early pregnancy (238 lncRNAs are differentially expressed in the olfactory bulb), but others do not. Enrichment analysis showed that differentially expressed lncRNAs from the olfactory bulb are co-expressed with genes previously linked to behavioral changes related to pregnancy. These findings provide a first characterization of the landscape of lncRNA expression in the goat brain and provides valuable clues to understand the molecular events triggered by early pregnancy in the central nervous system.
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Affiliation(s)
- Endika Varela-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B. Sarriena, Leioa 48940, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Encarna Casas
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Jaume Gardela
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Maria Jesús Palomo
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchebuchi Ike Osuagwuh
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchechi Linda Ohaneje
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department de Ciència Animal I dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Liu B, Shen CC, Xia SW, Song SS, Su LH, Li Y, Hao Q, Liu YJ, Guan DL, Wang N, Wang WJ, Zhao X, Li HX, Li XX, Lai YS. A nanopore-based cucumber genome assembly reveals structural variations at two QTLs controlling hypocotyl elongation. PLANT PHYSIOLOGY 2024; 195:970-985. [PMID: 38478469 DOI: 10.1093/plphys/kiae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 06/02/2024]
Abstract
The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.
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Affiliation(s)
- Bin Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, 830091 Urumqi, China
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cheng-Cheng Shen
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Shi-Wei Xia
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Shan-Shan Song
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Li-Hong Su
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Qian Hao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Yan-Jun Liu
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Dai-Lu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ning Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Wen-Jiao Wang
- College of Horticulture, Shanxi Agricultural University, 030801 Jinzhong, China
| | - Xiang Zhao
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Huan-Xiu Li
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
| | - Xi-Xiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100080 Beijing, China
| | - Yun-Song Lai
- College of Horticulture, Sichuan Agricultural University, 611130 Chengdu, China
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Wu J, Tang W, Li Z, Chakraborty A, Zhou C, Li F, He S. Duplications and Losses of the Detoxification Enzyme Glycosyltransferase 1 Are Related to Insect Adaptations to Plant Feeding. Int J Mol Sci 2024; 25:6080. [PMID: 38892266 PMCID: PMC11173166 DOI: 10.3390/ijms25116080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Insects have developed sophisticated detoxification systems to protect them from plant secondary metabolites while feeding on plants to obtain necessary nutrients. As an important enzyme in the system, glycosyltransferase 1 (GT1) conjugates toxic compounds to mitigate their harm to insects. However, the evolutionary link between GT1s and insect plant feeding remains elusive. In this study, we explored the evolution of GT1s across different insect orders and feeding niches using publicly available insect genomes. GT1 is widely present in insect species; however, its gene number differs among insect orders. Notably, plant-sap-feeding species have the highest GT1 gene numbers, whereas blood-feeding species display the lowest. GT1s appear to be associated with insect adaptations to different plant substrates in different orders, while the shift to non-plant feeding is related to several losses of GT1s. Most large gene numbers are likely the consequence of tandem duplications showing variations in collinearity among insect orders. These results reveal the potential relationships between the evolution of GT1s and insect adaptation to plant feeding, facilitating our understanding of the molecular mechanisms underlying insect-plant interactions.
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Affiliation(s)
- Jinyu Wu
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Wanjiang Tang
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Zhengyang Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic;
| | - Cao Zhou
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Fei Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Shulin He
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
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Muterko A, Kiseleva A, Salina E. A Transcriptome Response of Bread Wheat ( Triticum aestivum L.) to a 5B Chromosome Substitution from Wild Emmer. PLANTS (BASEL, SWITZERLAND) 2024; 13:1514. [PMID: 38891322 PMCID: PMC11174853 DOI: 10.3390/plants13111514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/16/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Over the years, alien chromosome substitution has attracted the attention of geneticists and breeders as a rich source of remarkable genetic diversity for improvement in narrowly adapted wheat cultivars. One of the problems encountered along this way is the coadaptation and realization of the genome of common wheat against the background of the introduced genes. Here, using RNA-Seq, we assessed a transcriptome response of hexaploid wheat Triticum aestivum L. (cultivar Chinese Spring) to a 5B chromosome substitution with its homolog from wild emmer (tetraploid wheat T. dicoccoides Koern) and discuss how complete the physiological compensation for this alien chromatin introgression is. The main signature of the transcriptome in the substituted line was a sharp significant drop of activity before the beginning of the photoperiod with a gradual increase up to overexpression in the middle of the night. The differential expression altered almost all biological processes and pathways tested. Because in most cases, the differential expression or its fold change were modest, and this was only a small proportion of the expressed transcriptome, the physiological compensation of the 5B chromosome substitution in common wheat seemed overall satisfactory, albeit not completely. No over- or under-representation of differential gene expression was found in specific chromosomes, implying that local structural changes in the genome can trigger a global transcriptome response.
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Affiliation(s)
- Alexandr Muterko
- Institute of Cytology and Genetics SB RAS, 10 Akad. Lavrentyeva Avenue, Novosibirsk 630090, Russia
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Lin X, Yin J, Wang Y, Yao J, Li QQ, Latzel V, Bossdorf O, Zhang YY. Environment-induced heritable variations are common in Arabidopsis thaliana. Nat Commun 2024; 15:4615. [PMID: 38816460 PMCID: PMC11139905 DOI: 10.1038/s41467-024-49024-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yifan Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA
| | - Vit Latzel
- Institute of Botany of the CAS, Zamek 1, 252 43, Pruhonice, Czech Republic
| | - Oliver Bossdorf
- Institute of Evolution & Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
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Zhong Y, Luo Y, Sun J, Qin X, Gan P, Zhou Z, Qian Y, Zhao R, Zhao Z, Cai W, Luo J, Chen LL, Song JM. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice. THE PLANT CELL 2024; 36:2117-2139. [PMID: 38345423 PMCID: PMC11132889 DOI: 10.1093/plcell/koae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/19/2024] [Indexed: 05/30/2024]
Abstract
Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
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Affiliation(s)
- Yuanyuan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinliang Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xuemei Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ping Gan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zuwen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yongqing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Rupeng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhiyuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jijing Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jia-Ming Song
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Hartley GA, Frankenberg SR, Robinson NM, MacDonald AJ, Hamede RK, Burridge CP, Jones ME, Faulkner T, Shute H, Rose K, Brewster R, O'Neill RJ, Renfree MB, Pask AJ, Feigin CY. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Commun Biol 2024; 7:636. [PMID: 38796620 PMCID: PMC11128018 DOI: 10.1038/s42003-024-06251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/26/2024] [Indexed: 05/28/2024] Open
Abstract
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Natasha M Robinson
- Fenner School of Environment & Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Anna J MacDonald
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, 7050, Australia
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Tim Faulkner
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Hayley Shute
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW, 2088, Australia
| | - Rob Brewster
- WWF-Australia, PO Box 528, Sydney, NSW, 2001, Australia
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Sciences, Museums Victoria, Carlton, VIC, 3053, Australia
| | - Charles Y Feigin
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC, 3086, Australia.
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49
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
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Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
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50
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Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol 2024:10.1038/s41587-024-02245-9. [PMID: 38778214 DOI: 10.1038/s41587-024-02245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson's disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - J Anthony Brandon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Madeline L Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Kayla A Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ketsile I Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Brendan J White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Lacey A Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Grant A Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mark E Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Patricia H Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Brittney A Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- UK Dementia Research Institute at The University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA.
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA.
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