1
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Choi TJ, Malik A, Han SM, Kim CB. Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones. BMC Genomics 2024; 25:725. [PMID: 39060996 PMCID: PMC11282837 DOI: 10.1186/s12864-024-10643-1] [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: 04/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress. RESULTS KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype. CONCLUSIONS Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.
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Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Korea
| | - Seung-Min Han
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, Korea.
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2
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Shikina S, Yoshioka Y, Chiu YL, Uchida T, Chen E, Cheng YC, Lin TC, Chu YL, Kanda M, Kawamitsu M, Fujie M, Takeuchi T, Zayasu Y, Satoh N, Shinzato C. Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp. Commun Biol 2024; 7:899. [PMID: 39048698 PMCID: PMC11269664 DOI: 10.1038/s42003-024-06544-4] [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: 12/21/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.
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Affiliation(s)
- Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yi-Ling Chiu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Emma Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yin-Chu Cheng
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzu-Chieh Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Ling Chu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Miyuki Kanda
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.
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3
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Schneider K, Steward RA, Celorio-Mancera MDLP, Janz N, Moberg D, Wheat CW, Nylin S. Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album). Mol Ecol 2024:e17479. [PMID: 39036890 DOI: 10.1111/mec.17479] [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: 02/20/2024] [Revised: 05/30/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024]
Abstract
Generalist plant-feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host-specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c-album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade-offs in the evolution of host plant repertoires.
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Affiliation(s)
| | - Rachel A Steward
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Biology Department, Lund University, Lund, Sweden
| | - Maria de la Paz Celorio-Mancera
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Ecology, Environment and Plant Science, Stockholm University, Stockholm, Sweden
| | - Niklas Janz
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Dick Moberg
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Sören Nylin
- Department of Zoology, Stockholm University, Stockholm, Sweden
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4
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Li ST, Ke Y, Zhu Y, Zhu TY, Huang H, Li L, Hou Z, Zhang X, Li Y, Liu C, Li X, Xie M, Zhou L, Meng C, Wang F, Gu X, Yang B, Yu H, Liang Z. Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N 6-methyladenosine. NATURE PLANTS 2024:10.1038/s41477-024-01745-5. [PMID: 38997433 DOI: 10.1038/s41477-024-01745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome.
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Affiliation(s)
- Shang-Tong Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Glbizzia Biosciences, Beijing, China
| | - Yunzhuo Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunke Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tian-Yi Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huanwei Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linxia Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyang Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuemin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaping Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaofan Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiulan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Faming Wang
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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5
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Guisasola-Serrano A, Bilbao-Arribas M, Varela-Martínez E, Abendaño N, Pérez M, Luján L, Jugo BM. Identifying transcriptomic profiles in ovine spleen after repetitive vaccination. Front Immunol 2024; 15:1386590. [PMID: 39076984 PMCID: PMC11284609 DOI: 10.3389/fimmu.2024.1386590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
Aluminum hydroxide has long been employed as a vaccine adjuvant for its safety profile, although its precise mechanism of action remains elusive. In this study, we investigated the transcriptomic responses in sheep spleen following repetitive vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. Notably, this work represents the first exploration of the sheep spleen transcriptome in such conditions. Animals were splitted in 3 treatment groups: vaccine group, adjuvant alone group and control group. A total of 18 high-depth RNA-seq libraries were sequenced, resulting in a rich dataset which also allowed isoform-level analysis. The comparisons between vaccine-treated and control groups (V vs C) as well as between vaccine-treated and adjuvant-alone groups (V vs A) revealed significant alterations in gene expression profiles, including protein coding genes and long non-coding RNAs. Among the differentially expressed genes, many were associated with processes such as endoplasmic reticulum (ER) stress, immune response and cell cycle. The analysis of co-expression modules further indicated a correlation between vaccine treatment and genes related to ER stress and unfolded protein response. Surprisingly, adjuvant-alone treatment had little impact on the spleen transcriptome. Additionally, the role of alternative splicing in the immune response was explored. We identified isoform switches in genes associated with immune regulation and inflammation, potentially influencing protein function. In conclusion, this study provides valuable insights into the transcriptomic changes in sheep spleen following vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. These findings shed light on the molecular mechanisms underlying vaccine-induced immune responses and emphasize the significance of antigenic components in aluminum adjuvant mechanism of action. Furthermore, the analysis of alternative splicing revealed an additional layer of complexity in the immune response to vaccination in a livestock species.
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Affiliation(s)
- Aitor Guisasola-Serrano
- Genetics, Physical Anthropology and Animal Physiology Dpt., Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Martin Bilbao-Arribas
- Genetics, Physical Anthropology and Animal Physiology Dpt., Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Endika Varela-Martínez
- Genetics, Physical Anthropology and Animal Physiology Dpt., Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Naiara Abendaño
- Genetics, Physical Anthropology and Animal Physiology Dpt., Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Marta Pérez
- Animal Pathology Dpt., Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
| | - Lluís Luján
- Animal Pathology Dpt., Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
| | - Begoña Marina Jugo
- Genetics, Physical Anthropology and Animal Physiology Dpt., Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
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6
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Lyu H, Moya ND, Andersen EC, Chamberlin HM. Gene duplication and evolutionary plasticity of lin-12/Notch gene function in Caenorhabditis. Genetics 2024; 227:iyae064. [PMID: 38809718 DOI: 10.1093/genetics/iyae064] [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: 01/10/2024] [Accepted: 04/16/2024] [Indexed: 05/31/2024] Open
Abstract
Gene duplication is an important substrate for the evolution of new gene functions, but the impacts of gene duplicates on their own activities and on the developmental networks in which they act are poorly understood. Here, we use a natural experiment of lin-12/Notch gene duplication within the nematode genus Caenorhabditis, combined with characterization of loss- and gain-of-function mutations, to uncover functional distinctions between the duplicate genes in 1 species (Caenorhabditis briggsae) and their single-copy ortholog in Caenorhabditis elegans. First, using improved genomic sequence and gene model characterization, we confirm that the C. briggsae genome includes 2 complete lin-12 genes, whereas most other genes encoding proteins that participate in the LIN-12 signaling pathway retain a one-to-one orthology with C. elegans. We use CRISPR-mediated genome editing to introduce alleles predicted to cause gain-of-function (gf) or loss-of-function (lf) into each C. briggsae gene and find that the gf mutations uncover functional distinctions not apparent from the lf alleles. Specifically, Cbr-lin-12.1(gf), but not Cbr-lin-12.2(gf), causes developmental defects similar to those observed in Cel-lin-12(gf). In contrast to Cel-lin-12(gf), however, the Cbr-lin-12.1(gf) alleles do not cause dominant phenotypes as compared to the wild type, and the mutant phenotype is observed only when 2 gf alleles are present. Our results demonstrate that gene duplicates can exhibit differential capacities to compensate for each other and to interfere with normal development, and uncover coincident gene duplication and evolution of developmental sensitivity to LIN-12/Notch activity.
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Affiliation(s)
- Haimeng Lyu
- Department of Molecular Genetics, Ohio State University, 484 W 12th Ave, Columbus, OH 43210, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Bascom UTL 383, 3400 North Charles St., Baltimore, MD 21218, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Bascom UTL 383, 3400 North Charles St., Baltimore, MD 21218, USA
| | - Helen M Chamberlin
- Department of Molecular Genetics, Ohio State University, 484 W 12th Ave, Columbus, OH 43210, USA
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7
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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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8
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Nath P, Bhuyan K, Bhattacharyya DK, Barah P. ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks. Comput Biol Chem 2024; 112:108140. [PMID: 38996755 DOI: 10.1016/j.compbiolchem.2024.108140] [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: 08/31/2023] [Revised: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024]
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in the regulation of gene expression and maintenance of genomic integrity through various interactions with DNA, RNA, and proteins. The availability of large-scale sequence data from various high-throughput platforms has opened possibilities to identify, predict, and functionally annotate lncRNAs. As a result, there is a growing demand for an integrative computational framework capable of identifying known lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding), a user-friendly, integrative, open-source, scalable, and modular computational framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC employs six stringent filtration steps to identify novel lncRNAs, performs differential expression analysis of mRNA and lncRNA transcripts, and predicts regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked ETENLNC against six existing tools and optimized it for desktop workstations and high-performance computing environments using data from three different species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.
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Affiliation(s)
- Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India
| | - Kaveri Bhuyan
- Department of Computer Science and Engineering, Tezpur University, Assam 784028, India; Department of Electrical Engineering, Tezpur University, Assam 784028, India
| | | | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India.
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9
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Carbonell-Sala S, Perteghella T, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nat Commun 2024; 15:5278. [PMID: 38937428 PMCID: PMC11211341 DOI: 10.1038/s41467-024-49523-3] [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: 07/12/2023] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we develop CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5' capped, full-length transcripts. In our study, we evaluate the performance of CapTrap-seq alongside other widely used RNA-seq library preparation protocols in human and mouse tissues, employing both ONT and PacBio sequencing technologies. To explore the quantitative capabilities of CapTrap-seq and its accuracy in reconstructing full-length RNA molecules, we implement a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation. Our benchmarks, incorporating the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) data, demonstrate that CapTrap-seq is a competitive, platform-agnostic RNA library preparation method for generating full-length transcript sequences.
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Affiliation(s)
- Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Tamara Perteghella
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Flomics Biotech, SL, Carrer de Roc Boronat 31, 08005, Barcelona, Catalonia, Spain
| | - Hiromi Nishiyori
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
- Human Technopole, Milan, Italy
| | - Barbara Uszczynska-Ratajczak
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Department of Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
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10
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Wang S, Shi Y, Zhou Y, Hu W, Liu F. Full-length transcriptome sequencing of Arabidopsis plants provided new insights into the autophagic regulation of photosynthesis. Sci Rep 2024; 14:14588. [PMID: 38918488 PMCID: PMC11199623 DOI: 10.1038/s41598-024-65555-7] [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: 03/08/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
Autophagy is a highly conserved eukaryotic pathway and plays a crucial role in cell survival under stress conditions. Here, we applied a full-length transcriptome approach to study an Arabidopsis autophagy mutant (atg5-1) subjected to nitrogen-starvation, using Oxford Nanopore Technologies. A total of 39,033 transcripts were identified, including 11,356 new transcripts. In addition, alternative splicing (AS) events and lncRNAs were also detected between Col-0 (WT) and atg5-1. Differentially expressed transcript enrichment showed that autophagy upregulates the expression of many stress-responsive genes and inhibits the transcription of photosynthesis-associated genes. The qRT-PCR results showed that the expression patterns of photosynthesis-related genes in the atg5-1 differed under the conditions of nitrogen starvation and carbon starvation. Under nitrogen starvation treatment, many genes related to photosynthesis also exhibited AS. Chlorophyll fluorescence images revealed that the Fv/Fm and ΦPSII of old atg5-1 leaves were significantly reduced after nitrogen starvation treatment, but the Y(NPQ) indices were significantly increased compared to those of the WT plants. The results of qRT-PCR suggest that autophagy appears to be involved in the degradation of genes related to photodamage repair in PSII. Taken together, the full-length transcriptiome sequencing provide new insights into how new transcripts, lncRNAs and alternative splicing (AS) are involved in plant autophagy through full-length transcriptome sequencing and suggest a new potential link between autophagy and photosynthesis.
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Affiliation(s)
- Song Wang
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Yunfeng Shi
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Yanhui Zhou
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
- College of Life Science, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China.
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China.
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11
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Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M, Vellutini BC, Larsson T, Savage EL, Lopez MO, Hercog R, Provaznik J, Ordoñez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Özpolat BD, Arendt D. A genome resource for the marine annelid Platynereis dumerilii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600153. [PMID: 38948846 PMCID: PMC11213123 DOI: 10.1101/2024.06.21.600153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii and of the closely related P. massiliensis and P. megalops, to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 580 miRNA loci. We further explore the high genetic variation (~3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.
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Affiliation(s)
- Kevin Nzumbi Mutemi
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Austria
| | - Leslie Pan
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Luca Santangeli
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ryan W. Null
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Mette Handberg-Thorsager
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | | | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Current: Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Emily L. Savage
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Current: Centre for Organismal Studies, University of Heidelberg, Heidelberg
| | - Mireia Osuna Lopez
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rajna Hercog
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany - not at EMBL anymore, do not know current address
| | - Jan Provaznik
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France. - deceased
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Vladimir Benes
- EMBL, Genomics Core Facility, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Conrad Helm
- Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - B. Duygu Özpolat
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Centre for Organismal Studies (COS) University of Heidelberg, 69120 Heidelberg, Germany
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12
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Sugiura K, Yoshida Y, Hayashi K, Arakawa K, Kunieda T, Matsumoto M. Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome. ZOOLOGICAL LETTERS 2024; 10:11. [PMID: 38902818 PMCID: PMC11191345 DOI: 10.1186/s40851-024-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND In gonochoristic animals, the sex determination pathway induces different morphological and behavioral features that can be observed between sexes, a condition known as sexual dimorphism. While many components of this sex differentiation cascade show high levels of diversity, factors such as the Doublesex-Mab-3-Related Transcription factor (DMRT) are widely conserved across animal taxa. Species of the phylum Tardigrada exhibit remarkable diversity in morphology and behavior between sexes, suggesting a pathway regulating this dimorphism. Despite the wealth of genomic and zoological knowledge accumulated in recent studies, the sexual differences in tardigrades genomes have not been identified. In the present study, we focused on the gonochoristic species Paramacrobiotus metropolitanus and employed omics analyses to unravel the molecular basis of sexual dimorphism. RESULTS Transcriptome analysis between sex-identified specimens revealed numerous differentially expressed genes, of which approximately 2,000 male-biased genes were focused on 29 non-male-specific genomic loci. From these regions, we identified two Macrobiotidae family specific DMRT paralogs, which were significantly upregulated in males and lacked sex specific splicing variants. Furthermore, phylogenetic analysis indicated all tardigrade genomes lack the doublesex ortholog, suggesting doublesex emerged after the divergence of Tardigrada. In contrast to sex-specific expression, no evidence of genomic differences between the sexes was found. We also identified several anhydrobiosis genes that exhibit sex-biased expression, suggesting a possible mechanism for protection of sex-specific tissues against extreme stress. CONCLUSIONS This study provides a comprehensive analysis for analyzing the genetic differences between sexes in tardigrades. The existence of male-biased, but not male-specific, genomic loci and identification of the family specific male-biased DMRT subfamily provides the foundation for understanding the sex determination cascade. In addition, sex-biased expression of several tardigrade-specific genes which are involved their stress tolerance suggests a potential role in protecting sex-specific tissue and gametes.
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Affiliation(s)
- Kenta Sugiura
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Yoshida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kohei Hayashi
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihoji, Tsuruoka, Yamagata, 997-0017, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Takekazu Kunieda
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Midori Matsumoto
- Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama, Kanagawa, 223-8522, Japan.
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13
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Wang Q, Zhang J, Liu C, Ru C, Qian Q, Yang M, Yan S, Liu W, Wang G. Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis. Front Physiol 2024; 15:1384426. [PMID: 38952867 PMCID: PMC11215311 DOI: 10.3389/fphys.2024.1384426] [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: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
Alternative splicing is an essential post-transcriptional regulatory mechanism that diversifies gene function by generating multiple protein isoforms from a single gene and act as a crucial role in insect environmental adaptation. Olfaction, a key sense for insect adaptation, relies heavily on the antennae, which are the primary olfactory organs expressing most of the olfactory genes. Despite the extensive annotation of olfactory genes within insect antennal tissues facilitated by high-throughput sequencing technology advancements, systematic analyses of alternative splicing are still relatively less. In this study, we focused on the oriental fruit fly (Bactrocera dorsalis), a significant pest of fruit crops. We performed a detailed analysis of alternative splicing in its antennae by utilizing the full-length transcriptome of its antennal tissue and the insect's genome. The results revealed 8600 non-redundant full-length transcripts identified in the oriental fruit fly antennal full-length transcriptome, spanning 4,145 gene loci. Over 40% of these loci exhibited multiple isoforms. Among these, 161 genes showed sex-biased isoform switching, involving seven different types of alternative splicing. Notably, events involving alternative transcription start sites (ATSS) and alternative transcription termination sites (ATTS) were the most common. Of all the genes undergoing ATSS and ATTS alternative splicing between male and female, 32 genes were alternatively spliced in protein coding regions, potentially affecting protein function. These genes were categorized based on the length of the sex-biased isoforms, with the highest difference in isoform fraction (dIF) associated with the ATSS type, including genes such as BdorABCA13, BdorCAT2, and BdorTSN3. Additionally, transcription factor binding sites for doublesex were identified upstream of both BdorABCA13 and BdorCAT2. Besides being expressed in the antennal tissues, BdorABCA13 and BdorCAT2 are also expressed in the mouthparts, legs, and genitalia of both female and male adults, suggesting their functional diversity. This study reveals alternative splicing events in the antennae of Bactrophora dorsalis from two aspects: odorant receptor genes and other types of genes expressed in the antennae. This study not only provides a research foundation for understanding the regulation of gene function by alternative splicing in the oriental fruit fly but also offers new insights for utilizing olfaction-based behavioral manipulation techniques to manage this pest.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jie Zhang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chenhao Liu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chuanjian Ru
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Qian Qian
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Minghuan Yang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shanchun Yan
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin, China
| | - Wei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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14
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Collins JE, Jiang T, Lee JW, Wendt K, Nardella F, Jeon J, Paes R, Santos NM, Rocamora F, Chang M, Schaefer S, Cichewicz RH, Winzeler EA, Chakrabarti D. Understanding the Antiplasmodial Action of Resistance-Refractory Xanthoquinodin A1. ACS Infect Dis 2024; 10:2276-2287. [PMID: 38810215 DOI: 10.1021/acsinfecdis.4c00232] [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] [Indexed: 05/31/2024]
Abstract
Our previous work identified a series of 12 xanthoquinodin analogues and 2 emodin-dianthrones with broad-spectrum activities against Trichomonas vaginalis, Mycoplasma genitalium, Cryptosporidium parvum, and Plasmodium falciparum. Analyses conducted in this study revealed that the most active analogue, xanthoquinodin A1, also inhibits Toxoplasma gondii tachyzoites and the liver stage of Plasmodium berghei, with no cross-resistance to the known antimalarial targets PfACS, PfCARL, PfPI4K, or DHODH. In Plasmodium, inhibition occurs prior to multinucleation and induces parasite death following 12 h of compound exposure. This moderately fast activity has impeded resistance line generation, with xanthoquinodin A1 demonstrating an irresistible phenotype in both T. gondii and P. falciparum.
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Affiliation(s)
- Jennifer E Collins
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Tiantian Jiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Jin Woo Lee
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Karen Wendt
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Flore Nardella
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Jin Jeon
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Raphaella Paes
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Natalia Mojica Santos
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Maya Chang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Samuel Schaefer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, 12722 Research Parkway, Orlando, Florida 32826, United States
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15
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Tariq A, Meng M, Jiang X, Bolger A, Beier S, Buchmann JP, Fernie AR, Wen W, Usadel B. In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38872506 DOI: 10.1111/tpj.16874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 06/15/2024]
Abstract
Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health-related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple-leaved assamica cultivar "Zijuan", the temperature-sensitive sinensis cultivar "Anjibaicha" and the wild accession "L618" whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene-centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene-centric variants, especially for Anthocyanidin synthases. We constructed a gene-centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.
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Affiliation(s)
- Arslan Tariq
- HHU Düsseldorf, Faculty of Mathematics and Natural Sciences, CEPLAS, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany
| | - Minghui Meng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohui Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Anthony Bolger
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, CEPLAS, Forschungszentrum Jülich, Leo Brandt-Straße, Jülich, 52425, Germany
| | - Sebastian Beier
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, CEPLAS, Forschungszentrum Jülich, Leo Brandt-Straße, Jülich, 52425, Germany
| | - Jan P Buchmann
- HHU Düsseldorf, Faculty of Mathematics and Natural Sciences, CEPLAS, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Weiwei Wen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- HHU Düsseldorf, Faculty of Mathematics and Natural Sciences, CEPLAS, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, Germany
- Institute of Bio- and Geosciences, IBG-4: Bioinformatics, CEPLAS, Forschungszentrum Jülich, Leo Brandt-Straße, Jülich, 52425, Germany
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16
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Wan L, Su S, Liu J, Zou B, Jiang Y, Jiao B, Tang S, Zhang Y, Deng C, Xiao W. The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles. Evol Bioinform Online 2024; 20:11769343241261814. [PMID: 38883803 PMCID: PMC11179516 DOI: 10.1177/11769343241261814] [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: 03/04/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Background Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.
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Affiliation(s)
- Linrong Wan
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Siyuan Su
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Jinyun Liu
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Bangxing Zou
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yaming Jiang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Beibei Jiao
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Shaokuan Tang
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Youhong Zhang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Cao Deng
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Wenfu Xiao
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
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17
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Zhang L, Liu X, Li W, Liu K, Zhang J, Liu X, Wang J. Integrative transcriptomic profiling of ncRNAs and mRNAs in developing mouse lens. Front Genet 2024; 15:1405715. [PMID: 38933921 PMCID: PMC11199715 DOI: 10.3389/fgene.2024.1405715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
In recent years, burgeoning research has underscored the pivotal role of non-coding RNA in orchestrating the growth, development, and pathogenesis of various diseases across organisms. However, despite these advances, our understanding of the specific contributions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) to lens development remains notably limited. Clarifying the intricate gene regulatory networks is imperative for unraveling the molecular underpinnings of lens-related disorders. In this study, we aimed to address this gap by conducting a comprehensive analysis of the expression profiles of messenger RNAs (mRNAs), lncRNAs, and circRNAs at critical developmental time points of the mouse lens, encompassing both embryonic (E10.5, E12.5, and E16.5) and postnatal stages (P0.5, P10.5, and P60). Leveraging RNA-sequencing technology, we identified key transcripts pivotal to lens development. Our analysis revealed differentially expressed (DE) mRNAs, lncRNAs, and circRNAs across various developmental stages. Particularly noteworthy, there were 1831 co-differentially expressed (CO-DE) mRNAs, 150 CO-DE lncRNAs, and 13 CO-DE circRNAs identified during embryonic stages. Gene Ontology (GO) enrichment analysis unveiled associations primarily related to lens development, DNA conformational changes, and angiogenesis among DE mRNAs and lncRNAs. Furthermore, employing protein-protein interaction networks, mRNA-lncRNA co-expression networks, and circRNA-microRNA-mRNA networks, we predicted candidate key molecules implicated in lens development. Our findings underscore the pivotal roles of lncRNAs and circRNAs in this process, offering fresh insights into the pathogenesis of lens-related disorders and paving the way for future exploration in this field.
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Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, General Hospital of Central Theater Command, Wuhan, China
| | - Xin Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Wei Li
- Department of Pediatric Respiratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaiqing Liu
- The Department of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jing Zhang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Xinhua Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Jiantao Wang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
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18
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Vanamamalai VK, Priyanka E, Kannaki TR, Sharma S. Breed and timepoint-based analysis of chicken harderian gland transcriptome during Newcastle disease virus challenge. Front Mol Biosci 2024; 11:1365888. [PMID: 38915939 PMCID: PMC11194529 DOI: 10.3389/fmolb.2024.1365888] [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: 01/05/2024] [Accepted: 05/07/2024] [Indexed: 06/26/2024] Open
Abstract
Introduction: Newcastle disease is a highly infectious disease caused by the Newcastle Disease Virus (NDV) and has a devastating financial impact on the global chicken industry. It was previously established that Leghorn and Fayoumi breeds of chicken exhibit variable resistance against NDV infection. The harderian gland is the less studied tissue of the chicken, known to play an essential role in the immune response. Methods: Our previous study, we reported differential gene expression and long noncoding RNAs (lncRNAs) between challenged and non-challenged chickens in the Harderian gland transcriptomic data. Now, we report the analysis of the same data studying the differential expression patterns between Leghorn and Fayoumi and between different timepoints during disease. First, the pipeline FHSpipe was used for identification of lncRNAs, followed by differential expression analysis by edgeR (GLM), functional annotation by OmicsBox, co-expression analysis using WGCNA and finally validation of selected lncRNAs and co-expressing genes using qRT-PCR. Results: Here, we observed that Leghorn showed a higher number of upregulated immune-related genes than Fayoumi in timepoint-based analysis, especially during the initial stages. Surprisingly, Fayoumi, being comparatively resistant, showed little difference between challenged and non-challenged conditions and different time points of the challenge. The breed-based analysis, which compared Leghorn with Fayoumi in both challenged and non-challenged conditions separately, identified several immune-related genes and positive co-expressing cis lncRNAs to be upregulated in Fayoumi when compared to Leghorn in both challenged and non-challenged conditions. Discussion: The current study shows that Leghorn, being comparatively more susceptible to NDV than Fayoumi, showed several immune-related genes and positive co-expressing cis lncRNAs upregulated in challenged Leghorn when compared to non-challenged Leghorn and also in different timepoints during challenge. While, breed-based analysis showed that there were more upregulated immune genes and positive cis-lncRNAs in Fayoumi than Leghorn. This result clearly shows that the differences in the expression of genes annotated with immune-related GO terms and pathways, i.e., immune-related genes and the co-expressing cis-lncRNAs between Leghorn and Fayoumi, and their role in the presence of differences in the resistance of Leghorn and Fayoumi chicken against NDV. Conclusion: These immune-genes and cis-lncRNAs could play a role in Fayoumi being comparatively more resistant to NDV than Leghorn. Our study elucidated the importance of lncRNAs during the host defense against NDV infection, paving the way for future research on the mechanisms governing the genetic improvement of chicken breeds.
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Affiliation(s)
- Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - E. Priyanka
- ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - T. R. Kannaki
- ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
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19
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Miao C, Wu Y, Wang L, Zhao S, Grierson D, Xu C, Chen W, Chen K. Haplotype-resolved chromosome-level genome assembly of Huyou (Citrus changshanensis). Sci Data 2024; 11:605. [PMID: 38849389 PMCID: PMC11161639 DOI: 10.1038/s41597-024-03437-3] [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: 12/25/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Huyou (Citrus changshanensis) is a significant citrus species that originated in Zhejiang Province, China, where it is also primarily cultivated. It is valued for its distinctive flavor and notable health benefits, owing to its high content of bioactive compounds like naringin and limonin. However, the absence of a high quality reference genome has limited the exploration of these health-promoting compounds in Huyou and hindered research into the mechanisms behind its medicinal properties. In this study, we present a phased chromosome-level genome assembly of Huyou. By combining PacBio and Hi-C sequencing, we generated a primary genome assembly and two haplotypes, comprising nine pseudo-chromosomes, with sizes of 339.91 Mb, 323.51 Mb, and 311.89 Mb, respectively. By integrating transcriptome data and annotations of homologous species, we identified a total of 29,775 protein-coding genes in the genome of Huyou. Additionally, we detected lots of structural variants between the two haplotypes. This represents the first reference genome of Huyou, providing a valuable resource for future studies on its agricultural characteristics and medicinal applications.
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Affiliation(s)
- Changjiu Miao
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yijing Wu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Lixia Wang
- Changshan Agricultural Characteristic Industry Development Center, Quzhou, 324000, China
| | - Siqing Zhao
- Changshan Agricultural Characteristic Industry Development Center, Quzhou, 324000, China
| | - Donald Grierson
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth and Development, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Changjie Xu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth and Development, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Wenbo Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China.
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth and Development, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China.
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth and Development, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Crop Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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20
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Bell AD, Paaby AB. A web application for gene-based queries of CaeNDR RNA-seq data. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001194. [PMID: 38911436 PMCID: PMC11193113 DOI: 10.17912/micropub.biology.001194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/01/2024] [Accepted: 06/04/2024] [Indexed: 06/25/2024]
Abstract
Variation in gene expression is a feature of all living systems and has recently been characterized extensively among wild strains of the model organism Caenorhabditis elegans. To enable researchers to query gene expression and gene expression variation at any gene of interest, we have created a user-friendly web application that shares RNA-seq transcription data for 208 wild C. elegans strains generated by the Caenorhabditis Natural Diversity Resource (CaeNDR). Here, we describe the features of the web application and the details of the data and data processing underlying it. We hope that this website, wildworm.biosci.gatech.edu/cendrexp/ , will help C. elegans researchers better understand their favorite genes and strains.
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States
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21
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Hakim JMC, Gutierrez Guarnizo SA, Málaga Machaca E, Gilman RH, Mugnier MR. Whole-genome assembly of a hybrid Trypanosoma cruzi strain assembled with Nanopore sequencing alone. G3 (BETHESDA, MD.) 2024; 14:jkae076. [PMID: 38592968 PMCID: PMC11152063 DOI: 10.1093/g3journal/jkae076] [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: 11/12/2023] [Revised: 11/12/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, which causes 10,000 deaths per year. Despite the high mortality associated with Chagas, relatively few parasite genomes have been assembled to date, with genome assemblies unavailable even for some commonly used laboratory strains. This is at least partially due to T. cruzi's highly complex and highly repetitive genome, which defies investigation using traditional short-read sequencing methods. In this study, we have generated a high-quality whole-genome assembly of the hybrid Tulahuen strain, a commercially available type VI strain, using long-read Nanopore sequencing without short-read scaffolding. The assembled genome contains 25% repeat regions, 17% variable multigene family members, and 27% transposable elements (TEs) and is of comparable quality with T. cruzi genome assemblies that utilized both long- and short-read data. Notably, we find that regions with TEs are significantly enriched for multicopy surface proteins, and that surface proteins are, on average, closer to TEs than to other coding regions. This finding suggests that mobile genetic elements such as transposons may drive recombination within surface protein gene families. This work demonstrates the feasibility of Nanopore sequencing to resolve complex regions of T. cruzi genomes, and with these resolved regions, provides support for a possible mechanism for genomic diversification.
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Affiliation(s)
- Jill M C Hakim
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Edith Málaga Machaca
- Asociación Benéfica PRISMA, Lima 15102, Peru
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Monica R Mugnier
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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22
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Xiong X, Xie C, Li S, Wang Y, Jiang J, Xie D, Chen S, Xiong Y, Gan L. PvGeneExpDB: An integrative gene expression database for in-depth understanding on the Pacific white shrimp (Litopenaeus vannamei). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101227. [PMID: 38518736 DOI: 10.1016/j.cbd.2024.101227] [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: 01/12/2024] [Revised: 02/27/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a high-valued economic farming species. With the development of high-throughput sequencing technology, cumulative large-scale transcriptomic studies have been revealing molecular landscape of various biological conditions including genetic selection, breeding, evolution, disease landscape, etc. However, no single experiment or databases allow thorough investigations of transcriptomic dynamics for these progressions. Meanwhile, the available datasets are often scattered and lack management. Here, we have established PvGeneExpDB, the first gene expression database for L. vannamei (www.bio-marine-scau.com/pv_ex/), which encompasses gene expression profiles, differential expression, and co-expression analyses under various biological conditions. Based on the analyses of 7 datasets, which include 53 samples with accurate and detailed records, PvGeneExpDB identifies 20,599 novel transcripts, shows expression profiles of a total of 20,817 genes, and implements Gene Ontology (GO) reconstruction of 76.7 % of these genes. Besides, 26 co-expressed groups were first identified by large-scale, cross-sample Weighted Gene Co-expression Network Analysis (WGCNA). By integrating the gene expression data in the database, our goal is to deepen the biological understanding of L. vannamei.
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Affiliation(s)
- Xi Xiong
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Chun Xie
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Sijun Li
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanzhi Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Junyang Jiang
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Dizhi Xie
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-sen University, Guangzhou, Guangdong 510006, China.
| | - Lian Gan
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, Guangdong 511464, China.
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23
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler EE, Phillippy AM. The complete sequence and comparative analysis of ape sex chromosomes. Nature 2024; 630:401-411. [PMID: 38811727 PMCID: PMC11168930 DOI: 10.1038/s41586-024-07473-2] [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: 11/17/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
Abstract
Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bornberg-Bauer
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health and Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Yong-Hwee E Loh
- University of California Santa Barbara, Santa Barbara, CA, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joana L Rocha
- University of California Berkeley, Berkeley, CA, USA
| | - Fedor Ryabov
- Masters Program in National Research, University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mario Ventura
- Università degli Studi di Bari Aldo Moro, Bari, Italy
| | | | - Alice C Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan E Eichler
- University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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24
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Wang H, Wei X, Mo C, Wei M, Li Y, Fan Y, Gu X, Zhang X, Zhang Y, Kong Q. Integrated full-length transcriptome and metabolome analysis reveals the defence response of melon to gummy stem blight. PLANT, CELL & ENVIRONMENT 2024; 47:1997-2010. [PMID: 38379450 DOI: 10.1111/pce.14865] [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: 12/01/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Gummy stem blight (GSB), a widespread disease causing great loss to cucurbit production, has become a major threat to melon cultivation. However, the melon-GSB interaction remains largely unknown. Here, full-length transcriptome and widely targeted metabolome were used to investigate the defence responses of resistant (PI511089) and susceptible (Payzawat) melon accessions to GSB pathogen infection at 24 h. The biosynthesis of secondary metabolites and MAPK signalling pathway were specifically enriched for differentially expressed genes in PI511890, while carbohydrate metabolism and amino acid metabolism were specifically enriched in Payzawat. More than 1000 novel genes were identified and MAPK signalling pathway was specifically enriched for them in PI511890. There were 11 793 alternative splicing events involving in the defence response to GSB. Totally, 910 metabolites were identified in Payzawat and PI511890, and flavonoids were the dominant metabolites. Integrated full-length transcriptome and metabolome analysis showed eriodictyol and oxalic acid were the potential marker metabolites for GSB resistance in melon. Moreover, posttranscription regulation was widely involved in the defence response of melon to GSB pathogen infection. These results not only improve our understanding on the interaction between melon and GSB, but also facilitate the genetic improvement of melon with GSB resistance.
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Affiliation(s)
- Haiyan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Xiaoying Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Changjuan Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Minghua Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yaqiong Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yuxin Fan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Xuejun Zhang
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yongbing Zhang
- Hami-Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
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25
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Inamo J, Suzuki A, Ueda MT, Yamaguchi K, Nishida H, Suzuki K, Kaneko Y, Takeuchi T, Hatano H, Ishigaki K, Ishihama Y, Yamamoto K, Kochi Y. Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms. Nat Commun 2024; 15:4285. [PMID: 38806455 PMCID: PMC11133395 DOI: 10.1038/s41467-024-48615-4] [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: 12/04/2022] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer's disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3'-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.
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Affiliation(s)
- Jun Inamo
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Biomedical Engineering Research Innovation Center, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Hiroshi Nishida
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yuko Kaneko
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Saitama Medical University, 38 Morohongo, Moroyama, Iruma, Saitama, 350-0495, Japan
| | - Hiroaki Hatano
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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Navandar M, Vennin C, Lutz B, Gerber S. Long non-coding RNAs expression and regulation across different brain regions in primates. Sci Data 2024; 11:545. [PMID: 38806530 PMCID: PMC11133376 DOI: 10.1038/s41597-024-03380-3] [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: 12/22/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Human and non-human primates have strikingly similar genomes, but they strongly differ in many brain-based processes (e.g., behaviour and cognition). While the functions of protein-coding genes have been extensively studied, rather little is known about the role of non-coding RNAs such as long non-coding RNAs (lncRNAs). Here, we predicted lncRNAs and analysed their expression pattern across different brain regions of human and non-human primates (chimpanzee, gorilla, and gibbon). Our analysis identified shared orthologous and non-orthologous lncRNAs, showing striking differences in the genomic features. Differential expression analysis of the shared orthologous lncRNAs from humans and chimpanzees revealed distinct expression patterns in subcortical regions (striatum, hippocampus) and neocortical areas while retaining a homogeneous expression in the cerebellum. Co-expression analysis of lncRNAs and protein-coding genes revealed massive proportions of co-expressed pairs in neocortical regions of humans compared to chimpanzees. Network analysis of co-expressed pairs revealed the distinctive role of the hub-acting orthologous lncRNAs in a region- and species-specific manner. Overall, our study provides novel insight into lncRNA driven gene regulatory landscape, neural regulation, brain evolution, and constitutes a resource for primate's brain lncRNAs.
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Affiliation(s)
- Mohit Navandar
- Institute for Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Constance Vennin
- Leibniz Institute for Resilience Research, 55122, Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research, 55122, Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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Zhou H, Su X, Song B. ACMGA: a reference-free multiple-genome alignment pipeline for plant species. BMC Genomics 2024; 25:515. [PMID: 38796435 PMCID: PMC11127342 DOI: 10.1186/s12864-024-10430-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: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND The short-read whole-genome sequencing (WGS) approach has been widely applied to investigate the genomic variation in the natural populations of many plant species. With the rapid advancements in long-read sequencing and genome assembly technologies, high-quality genome sequences are available for a group of varieties for many plant species. These genome sequences are expected to help researchers comprehensively investigate any type of genomic variants that are missed by the WGS technology. However, multiple genome alignment (MGA) tools designed by the human genome research community might be unsuitable for plant genomes. RESULTS To fill this gap, we developed the AnchorWave-Cactus Multiple Genome Alignment (ACMGA) pipeline, which improved the alignment of repeat elements and could identify long (> 50 bp) deletions or insertions (INDELs). We conducted MGA using ACMGA and Cactus for 8 Arabidopsis (Arabidopsis thaliana) and 26 Maize (Zea mays) de novo assembled genome sequences and compared them with the previously published short-read variant calling results. MGA identified more single nucleotide variants (SNVs) and long INDELs than did previously published WGS variant callings. Additionally, ACMGA detected significantly more SNVs and long INDELs in repetitive regions and the whole genome than did Cactus. Compared with the results of Cactus, the results of ACMGA were more similar to the previously published variants called using short-read. These two MGA pipelines identified numerous multi-allelic variants that were missed by the WGS variant calling pipeline. CONCLUSIONS Aligning de novo assembled genome sequences could identify more SNVs and INDELs than mapping short-read. ACMGA combines the advantages of AnchorWave and Cactus and offers a practical solution for plant MGA by integrating global alignment, a 2-piece-affine-gap cost strategy, and the progressive MGA algorithm.
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Affiliation(s)
- Huafeng Zhou
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, 266071, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, 266071, China.
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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28
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Mathur K, Singh B, Puria R, Nain V. In silico genome wide identification of long non-coding RNAs differentially expressed during Candida auris host pathogenesis. Arch Microbiol 2024; 206:253. [PMID: 38727738 DOI: 10.1007/s00203-024-03969-7] [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: 03/19/2024] [Accepted: 04/18/2024] [Indexed: 05/15/2024]
Abstract
Candida auris is an invasive fungal pathogen of high concern due to acquired drug tolerance against antifungals used in clinics. The prolonged persistence on biotic and abiotic surfaces can result in onset of hospital outbreaks causing serious health threat. An in depth understanding of pathology of C. auris is highly desirable for development of efficient therapeutics. Non-coding RNAs play crucial role in fungal pathology. However, the information about ncRNAs is scanty to be utilized. Herein our aim is to identify long noncoding RNAs with potent role in pathobiology of C. auris. Thereby, we analyzed the transcriptomics data of C. auris infection in blood for identification of potential lncRNAs with regulatory role in determining invasion, survival or drug tolerance under infection conditions. Interestingly, we found 275 lncRNAs, out of which 253 matched with lncRNAs reported in Candidamine, corroborating for our accurate data analysis pipeline. Nevertheless, we obtained 23 novel lncRNAs not reported earlier. Three lncRNAs were found to be under expressed throughout the course of infection, in the transcriptomics data. 16 of potent lncRNAs were found to be coexpressed with coding genes, emphasizing for their functional role. Noteworthy, these ncRNAs are expressed from intergenic regions of the genes associated with transporters, metabolism, cell wall biogenesis. This study recommends for possible association between lncRNA expression and C. auris pathogenesis.
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Affiliation(s)
- Kartavya Mathur
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Bharti Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Rekha Puria
- School of Biotechnology, Gautam Buddha University, Greater Noida, India.
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India.
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29
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Edet OU, Ubi BE, Ishii T. Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp. Sci Rep 2024; 14:10654. [PMID: 38724579 PMCID: PMC11082238 DOI: 10.1038/s41598-024-61062-x] [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: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Department of Crop Science, University of Calabar, PMB 1115, Calabar, Cross River State, Nigeria.
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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30
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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Figueroa Corona L, Allen BJ, Puiu D, Wright J, De La Torre AR, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A genome sequence for the threatened whitebark pine. G3 (BETHESDA, MD.) 2024; 14:jkae061. [PMID: 38526344 PMCID: PMC11075562 DOI: 10.1093/g3journal/jkae061] [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: 12/11/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Whitebark Pine Ecosystem Foundation, Missoula, MT 59808, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Meltzer
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- University of California Cooperative Extension, Central Sierra, Jackson, CA 95642, USA
| | - Daniela Puiu
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jessica Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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31
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Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL, Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature 2024; 629:127-135. [PMID: 38658750 PMCID: PMC11062917 DOI: 10.1038/s41586-024-07305-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
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Affiliation(s)
- Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zhuoxin Chen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Harsha Sen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Yao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Parwinder Kaur
- The University of Western Australia, Crawley, Western Australia, Australia
| | - Judy St Leger
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | | | | | - Greta Keller
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Thomas Sanger
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Chen J, Hu Z, Li P, Wang G, Wei H, Li Q, Fu B, Sun Y. Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways. Front Genet 2024; 15:1365285. [PMID: 38689653 PMCID: PMC11058841 DOI: 10.3389/fgene.2024.1365285] [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: 01/04/2024] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Hypoxia is a mounting problem that affects the world's freshwaters, with severe consequence for many species, including death and large economical loss. The hypoxia problem has increased recently due to the combined effects of water eutrophication and global warming. In this study, we investigated the transcriptome atlas for the bony fish Ancherythroculter nigrocauda under hypoxia for 1.5, 3, and 4.5 h and its recovery to normal oxygen levels in heart and brain tissues. We sequenced 21 samples for brain and heart tissues (a total of 42 samples) plus three control samples and obtained an average of 32.40 million raw reads per sample, and 95.24% mapping rate of the filtered clean reads. This robust transcriptome dataset facilitated the discovery of 52,428 new transcripts and 6,609 novel genes. In the heart tissue, the KEGG enrichment analysis showed that genes linked to the Vascular smooth muscle contraction and MAPK and VEGF signaling pathways were notably altered under hypoxia. Re-oxygenation introduced changes in genes associated with abiotic stimulus response and stress regulation. In the heart tissue, weighted gene co-expression network analysis pinpointed a module enriched in insulin receptor pathways that was correlated with hypoxia. Conversely, in the brain tissue, the response to hypoxia was characterized by alterations in the PPAR signaling pathway, and re-oxygenation influenced the mTOR and FoxO signaling pathways. Alternative splicing analysis identified an average of 27,226 and 28,290 events in the heart and brain tissues, respectively, with differential events between control and hypoxia-stressed groups. This study offers a holistic view of transcriptomic adaptations in A. nigrocauda heart and brain tissues under oxygen stress and emphasizes the role of gene expression and alternative splicing in the response mechanisms.
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Affiliation(s)
- Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Zhen Hu
- Hubei Provincial Fisheries Technology Extension Center, Wuhan, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Guiying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Huijie Wei
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Beide Fu
- Ruibiao (Wuhan) Biotechnology Co., Ltd, Wuhan, China
| | - Yanhong Sun
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [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: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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Deng L, Wang Q, Liu H, Jiang Y, Xu M, Xiang Y, Yang T, Yang S, Yan D, Li M, Zhao L, Zhao X, Wan K, He G, Mijiti X, Li G. Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China. Front Microbiol 2024; 15:1290227. [PMID: 38686109 PMCID: PMC11056549 DOI: 10.3389/fmicb.2024.1290227] [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: 09/07/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb. Methods This study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains. Results Lineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes (gyrA, rpoB, rpoC, katG, pncA, embB, gid, and cut1) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1. There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes. Conclusion This study revealed the ongoing selective evolution of Mtb. We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.
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Affiliation(s)
- Lele Deng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Quan Wang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Miao Xu
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yu Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Ting Yang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shuliu Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Di Yan
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Machao Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guangxue He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaokaiti Mijiti
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Yu Z, Gao Z, Zeng Y, Li M, Xu G, Ren M, Zhu Y, Liu D. A delayed and unsynchronized ovary development as revealed by transcriptome of brain and pituitary of Coilia nasus. Front Mol Biosci 2024; 11:1361386. [PMID: 38665935 PMCID: PMC11043543 DOI: 10.3389/fmolb.2024.1361386] [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: 12/25/2023] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Coilia nasus is an anadromous fish that has been successfully domesticated in the last decade due to its high economic value. The fish exhibits a delayed ovary development during the reproductive season, despite breeding and selection for five to six offspring. The molecular mechanism of the delayed ovary development is still unknown, so the obstacles have not been removed in the large-scale breeding program. This study aims to investigate the key genes regulating ovarian development by comparing the transcriptomes of ovarian-stage IV and stage II brain/pituitary of Coilia nasus. Ovarian stages were validated by histological sections. A total of 75,097,641 and 66,735,592 high-quality reads were obtained from brain and pituitary transcriptomes, respectively, and alternatively spliced transcripts associated with gonadal development were detected. Compared to ovarian Ⅱ- brain, 515 differentially expressed genes (DEGs) were upregulated and 535 DEGs were downregulated in ovarian Ⅳ- brain, whereas 470 DEGs were upregulated and 483 DEGs were downregulated in ovarian Ⅳ- pituitary compared to ovarian Ⅱ- pituitary. DEGs involved in hormone synthesis and secretion and in the GnRH signaling pathway were screened. Weighted gene co-expression network analysis identified gene co-expression modules that were positively correlated with ovarian phenotypic traits. The hub genes Smad4 and TRPC4 in the modules were co-expressed with DEGs including Kiss1 receptor and JUNB, suggesting that ovarian development is controlled by a hypothalamic-pituitary-gonadal axis. Our results have provided new insights that advance our understanding of the molecular mechanism of C. nasus reproductive functions and will be useful for future breeding.
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Affiliation(s)
- Ziyan Yu
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Zongshuai Gao
- Department of Transfusion Medicine, Shanghai Sixth People’s Hospital Afffiliated to Shanghai Jiao Tong University School of Medicinel, Shanghai, China
| | - Yun Zeng
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Mingyou Li
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Mingchun Ren
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yunxia Zhu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dong Liu
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
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Simon NM, Kim Y, Bautista DM, Dutton JR, Brem RB. Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549406. [PMID: 37503246 PMCID: PMC10370129 DOI: 10.1101/2023.07.18.549406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. As a complement, we used sequence analyses to find population-genomic signatures of selection in M. m. castaneus, at the upstream regions of the translation genes, including at transcription factor binding sites. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Together, our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.
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Affiliation(s)
- Noah M. Simon
- Biology of Aging Doctoral Program, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA 94720, USA
| | - Yujin Kim
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Diana M. Bautista
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley CA 94720
| | - James R. Dutton
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rachel B. Brem
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA 94720, USA
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Greshnova A, Pál K, Martinez JFI, Canzar S, Makova KD. Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587783. [PMID: 38617276 PMCID: PMC11014635 DOI: 10.1101/2024.04.02.587783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Y chromosomes of great apes harbor Ampliconic Genes (YAGs)-multi-copy gene families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species. We generated hybrid transcriptome assemblies by combining targeted long reads (Pacific Biosciences), untargeted long reads (Pacific Biosciences) and untargeted short reads (Illumina)and mapping them to the T2T reference genomes. Compared to the results from the reference-free approach, average transcript length was more than two times higher, and the total number of transcripts decreased three times, improving the quality of the assembled transcriptome. The reference-based transcriptome assemblies allowed us to differentiate transcripts originating from different Y chromosome gene copies and from their non-Y chromosome homologs. We identified two sources of transcriptome diversity-alternative splicing and gene duplication with subsequent diversification of gene copies. For each gene family, we detected transcribed pseudogenes along with protein-coding gene copies. We revealed previously unannotated gene copies of YAGs as compared to currently available NCBI annotations, as well as novel isoforms for annotated gene copies. This analysis paves the way for better understanding Y chromosome gene functions, which is important given their role in spermatogenesis.
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Affiliation(s)
- Aleksandra Greshnova
- Department of Biology, Penn State University, University Park, PA, USA
- Current address: Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Karol Pál
- Department of Biology, Penn State University, University Park, PA, USA
| | - Juan Francisco Iturralde Martinez
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, United States
- Huck Institutes of the Life Sciences. Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan Canzar
- Faculty of Informatics and Data Science, University of Regensburg, Regensburg, Germany
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA, USA
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De Jode A, Faria R, Formenti G, Sims Y, Smith TP, Tracey A, Wood JMD, Zagrodzka ZB, Johannesson K, Butlin RK, Leder EH. Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis. Genome Biol Evol 2024; 16:evae076. [PMID: 38584387 PMCID: PMC11050657 DOI: 10.1093/gbe/evae076] [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: 11/30/2023] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/09/2024] Open
Abstract
The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.
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Affiliation(s)
- Aurélien De Jode
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE 45296 Strömstad, Sweden
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
- Dauphin Island Sea Lab, Dauphin Island, AL, USA
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Giulio Formenti
- The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Timothy P Smith
- USDA Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jonathan M D Wood
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Zuzanna B Zagrodzka
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE 45296 Strömstad, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE 45296 Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Erica H Leder
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, SE 45296 Strömstad, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
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Jiang C, Li P, Ma Y, Yoneda N, Kawai K, Uehara S, Ohnishi Y, Suemizu H, Cao H. Comprehensive gene profiling of the metabolic landscape of humanized livers in mice. J Hepatol 2024; 80:622-633. [PMID: 38049085 PMCID: PMC10947884 DOI: 10.1016/j.jhep.2023.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND & AIMS The human liver transcriptome is complex and highly dynamic, e.g. one gene may produce multiple distinct transcripts, each with distinct posttranscriptional modifications. Direct knowledge of transcriptome dynamics, however, is largely obscured by the inaccessibility of the human liver to treatments and the insufficient annotation of the human liver transcriptome at transcript and RNA modification levels. METHODS We generated mice that carry humanized livers of identical genetic background and subjected them to representative metabolic treatments. We then analyzed the humanized livers with nanopore single-molecule direct RNA sequencing to determine the expression level, m6A modification and poly(A) tail length of all RNA transcript isoforms. Our system allows for the de novo annotation of human liver transcriptomes to reflect metabolic responses and for the study of transcriptome dynamics in parallel. RESULTS Our analysis uncovered a vast number of novel genes and transcripts. Our transcript-level analysis of human liver transcriptomes also identified a multitude of regulated metabolic pathways that were otherwise invisible using conventional short-read RNA sequencing. We revealed for the first time the dynamic changes in m6A and poly(A) tail length of human liver transcripts, many of which are transcribed from key metabolic genes. Furthermore, we performed comparative analyses of gene regulation between humans and mice, and between two individuals using the liver-specific humanized mice, revealing that transcriptome dynamics are highly species- and genetic background-dependent. CONCLUSION Our work revealed a complex metabolic response landscape of the human liver transcriptome and provides a novel resource to understand transcriptome dynamics of the human liver in response to physiologically relevant metabolic stimuli (https://caolab.shinyapps.io/human_hepatocyte_landscape/). IMPACT AND IMPLICATIONS Direct knowledge of the human liver transcriptome is currently very limited, hindering the overall understanding of human liver pathophysiology. We combined a liver-specific humanized mouse model and long-read direct RNA sequencing technology to establish a de novo annotation of the human liver transcriptome and identified a multitude of regulated metabolic pathways that were otherwise invisible using conventional technologies. The extensive regulatory information on human genes we provided could enable basic scientists to infer the pathological relevance of their genes of interest and physician scientists to better pinpoint the changes in metabolic networks underlying a specific pathophysiology.
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Affiliation(s)
- Chengfei Jiang
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Li
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yonghe Ma
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nao Yoneda
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Kenji Kawai
- Pathology Center, Translational Research and Contract Research Service Division, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Shotaro Uehara
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Yasuyuki Ohnishi
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Hiroshi Suemizu
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals (CIEA), 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Haiming Cao
- Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Willner DL, Paudel S, Halleran AD, Solini GE, Gray V, Saha MS. Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1. BMC Microbiol 2024; 24:107. [PMID: 38561651 PMCID: PMC10986025 DOI: 10.1186/s12866-024-03241-4] [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: 11/25/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. RESULTS By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production. CONCLUSIONS The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.
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Affiliation(s)
- Dana L Willner
- Data Science Program, William & Mary, Williamsburg, VA, USA
| | - Sudip Paudel
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Wyss Institute, Harvard University, Cambridge, MA, USA
| | - Andrew D Halleran
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Atalaya Capital Management, New York, NY, USA
| | - Grace E Solini
- Department of Biology, William & Mary, Williamsburg, VA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Veronica Gray
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Georgetown University School of Medicine, Washington, DC, USA
| | - Margaret S Saha
- Department of Biology, William & Mary, Williamsburg, VA, USA.
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Romeo-Cardeillac C, Trovero MF, Radío S, Smircich P, Rodríguez-Casuriaga R, Geisinger A, Sotelo-Silveira J. Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis. BMC Genomics 2024; 25:295. [PMID: 38509455 PMCID: PMC10953240 DOI: 10.1186/s12864-024-10170-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: 10/02/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Mammalian testis is a highly complex and heterogeneous tissue. This complexity, which mostly derives from spermatogenic cells, is reflected at the transcriptional level, with the largest number of tissue-specific genes and long noncoding RNAs (lncRNAs) compared to other tissues, and one of the highest rates of alternative splicing. Although it is known that adequate alternative-splicing patterns and stage-specific isoforms are critical for successful spermatogenesis, so far only a very limited number of reports have addressed a detailed study of alternative splicing and isoforms along the different spermatogenic stages. RESULTS In the present work, using highly purified stage-specific testicular cell populations, we detected 33,002 transcripts expressed throughout mouse spermatogenesis not annotated so far. These include both splice variants of already annotated genes, and of hitherto unannotated genes. Using conservative criteria, we uncovered 13,471 spermatogenic lncRNAs, which reflects the still incomplete annotation of lncRNAs. A distinctive feature of lncRNAs was their lower number of splice variants compared to protein-coding ones, adding to the conclusion that lncRNAs are, in general, less complex than mRNAs. Besides, we identified 2,794 unannotated transcripts with high coding potential (including some arising from yet unannotated genes), many of which encode unnoticed putative testis-specific proteins. Some of the most interesting coding splice variants were chosen, and validated through RT-PCR. Remarkably, the largest number of stage-specific unannotated transcripts are expressed during early meiotic prophase stages, whose study has been scarcely addressed in former transcriptomic analyses. CONCLUSIONS We detected a high number of yet unannotated genes and alternatively spliced transcripts along mouse spermatogenesis, hence showing that the transcriptomic diversity of the testis is considerably higher than previously reported. This is especially prominent for specific, underrepresented stages such as those of early meiotic prophase, and its unveiling may constitute a step towards the understanding of their key events.
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Affiliation(s)
- Carlos Romeo-Cardeillac
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - María Fernanda Trovero
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santiago Radío
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay
| | - Adriana Geisinger
- Laboratory of Molecular Biology of Reproduction, Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11,600, Montevideo, Uruguay.
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), 11,400, Montevideo, Uruguay.
| | - José Sotelo-Silveira
- Department of Genomics, IIBCE, 11,600, Montevideo, Uruguay.
- Department of Cell and Molecular Biology, Facultad de Ciencias, UdelaR, 11,400, Montevideo, Uruguay.
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Hasan MS, McElroy KE, Audino JA, Serb JM. Opsin expression varies across larval development and taxa in pteriomorphian bivalves. Front Neurosci 2024; 18:1357873. [PMID: 38562306 PMCID: PMC10982516 DOI: 10.3389/fnins.2024.1357873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Many marine organisms have a biphasic life cycle that transitions between a swimming larva with a more sedentary adult form. At the end of the first phase, larvae must identify suitable sites to settle and undergo a dramatic morphological change. Environmental factors, including photic and chemical cues, appear to influence settlement, but the sensory receptors involved are largely unknown. We targeted the protein receptor, opsin, which belongs to large superfamily of transmembrane receptors that detects environmental stimuli, hormones, and neurotransmitters. While opsins are well-known for light-sensing, including vision, a growing number of studies have demonstrated light-independent functions. We therefore examined opsin expression in the Pteriomorphia, a large, diverse clade of marine bivalves, that includes commercially important species, such as oysters, mussels, and scallops. Methods Genomic annotations combined with phylogenetic analysis show great variation of opsin abundance among pteriomorphian bivalves, including surprisingly high genomic abundance in many species that are eyeless as adults, such as mussels. Therefore, we investigated the diversity of opsin expression from the perspective of larval development. We collected opsin gene expression in four families of Pteriomorphia, across three distinct larval stages, i.e., trochophore, veliger, and pediveliger, and compared those to adult tissues. Results We found larvae express all opsin types in these bivalves, but opsin expression patterns are largely species-specific across development. Few opsins are expressed in the adult mantle, but many are highly expressed in adult eyes. Intriguingly, opsin genes such as retinochrome, xenopsins, and Go-opsins have higher levels of expression in the later larval stages when substrates for settlement are being tested, such as the pediveliger. Conclusion Investigating opsin gene expression during larval development provides crucial insights into their intricate interactions with the surroundings, which may shed light on how opsin receptors of these organisms respond to various environmental cues that play a pivotal role in their settlement process.
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Affiliation(s)
- Md Shazid Hasan
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Kyle E. McElroy
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Jorge A. Audino
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | - Jeanne M. Serb
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
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Billman ZP, Kovacs SB, Wei B, Kang K, Cissé OH, Miao EA. Caspase-1 activates gasdermin A in non-mammals. eLife 2024; 12:RP92362. [PMID: 38497531 PMCID: PMC10948149 DOI: 10.7554/elife.92362] [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] [Indexed: 03/19/2024] Open
Abstract
Gasdermins oligomerize to form pores in the cell membrane, causing regulated lytic cell death called pyroptosis. Mammals encode five gasdermins that can trigger pyroptosis: GSDMA, B, C, D, and E. Caspase and granzyme proteases cleave the linker regions of and activate GSDMB, C, D, and E, but no endogenous activation pathways are yet known for GSDMA. Here, we perform a comprehensive evolutionary analysis of the gasdermin family. A gene duplication of GSDMA in the common ancestor of caecilian amphibians, reptiles, and birds gave rise to GSDMA-D in mammals. Uniquely in our tree, amphibian, reptile, and bird GSDMA group in a separate clade than mammal GSDMA. Remarkably, GSDMA in numerous bird species contain caspase-1 cleavage sites like YVAD or FASD in the linker. We show that GSDMA from birds, amphibians, and reptiles are all cleaved by caspase-1. Thus, GSDMA was originally cleaved by the host-encoded protease caspase-1. In mammals the caspase-1 cleavage site in GSDMA is disrupted; instead, a new protein, GSDMD, is the target of caspase-1. Mammal caspase-1 uses exosite interactions with the GSDMD C-terminal domain to confer the specificity of this interaction, whereas we show that bird caspase-1 uses a stereotypical tetrapeptide sequence to confer specificity for bird GSDMA. Our results reveal an evolutionarily stable association between caspase-1 and the gasdermin family, albeit a shifting one. Caspase-1 repeatedly changes its target gasdermin over evolutionary time at speciation junctures, initially cleaving GSDME in fish, then GSDMA in amphibians/reptiles/birds, and finally GSDMD in mammals.
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Affiliation(s)
- Zachary Paul Billman
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Stephen Bela Kovacs
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Bo Wei
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Kidong Kang
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Ousmane H Cissé
- Critical Care Medicine Department, National Institutes of Health Clinical CenterBethesdaUnited States
| | - Edward A Miao
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
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Fuchs LIR, Knobloch J, Wiesenthal AA, Fuss J, Franzenburg S, Torres Oliva M, Müller C, Wheat CW, Hildebrandt JP. A draft genome of the neritid snail Theodoxus fluviatilis. G3 (BETHESDA, MD.) 2024; 14:jkad282. [PMID: 38069680 PMCID: PMC10917513 DOI: 10.1093/g3journal/jkad282] [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: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The neritid snail Theodoxus fluviatilis is found across habitats differing in salinity, from shallow waters along the coast of the Baltic Sea to lakes throughout Europe. Living close to the water surface makes this species vulnerable to changes in salinity in their natural habitat, and the lack of a free-swimming larval stage limits this species' dispersal. Together, these factors have resulted in a patchy distribution of quite isolated populations differing in their salinity tolerances. In preparation for investigating the mechanisms underlying the physiological differences in osmoregulation between populations that cannot be explained solely by phenotypic plasticity, we present here an annotated draft genome assembly for T. fluviatilis, generated using PacBio long reads, Illumina short reads, and transcriptomic data. While the total assembly size (1045 kb) is similar to those of related species, it remains highly fragmented (N scaffolds = 35,695; N50 = 74 kb) though moderately high in complete gene content (BUSCO single copy complete: 74.3%, duplicate: 2.6%, fragmented: 10.6%, missing: 12.5% using metazoa n = 954). Nevertheless, we were able to generate gene annotations of 21,220 protein-coding genes (BUSCO single copy complete: 65.1%, duplicate: 16.7%, fragmented: 9.1%, missing: 9.1% using metazoa n = 954). Not only will this genome facilitate comparative evolutionary studies across Gastropoda, as this is the first genome assembly for the basal snail family Neritidae, it will also greatly facilitate the study of salinity tolerance in this species. Additionally, we discuss the challenges of working with a species where high molecular weight DNA isolation is very difficult.
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Affiliation(s)
- Laura Iris Regina Fuchs
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Jan Knobloch
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Amanda Alice Wiesenthal
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
- Marine Biology, University of Rostock, Albert-Einstein-Straße 3, D - 18059 Rostock, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Soeren Franzenburg
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Montserrat Torres Oliva
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Christopher W Wheat
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, S-10691 Stockholm, Sweden
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
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Carpinteyro-Ponce J, Machado CA. The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes. Genome Biol Evol 2024; 16:evae047. [PMID: 38482945 PMCID: PMC10980976 DOI: 10.1093/gbe/evae047] [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] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.
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Affiliation(s)
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
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Amwoma JG, Kituyi S, Wakoli DM, Ochora DO, Chemwor G, Maisiba R, Okore W, Opot B, Juma D, Muok EM, Garges EC, Egbo TE, Nyabuga FN, Andagalu B, Akala HM. Comparative analysis of peripheral whole blood transcriptome from asymptomatic carriers reveals upregulation of subsets of surface proteins implicated in Plasmodium falciparum phenotypic plasticity. Biochem Biophys Rep 2024; 37:101596. [PMID: 38146350 PMCID: PMC10749222 DOI: 10.1016/j.bbrep.2023.101596] [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: 07/13/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
The molecular mechanism underlying Plasmodium falciparum's persistence in the asymptomatic phase of infection remains largely unknown. However, large-scale shifts in the parasites' gene expression during asymptomatic infections may enhance phenotypic plasticity, maximizing their fitness and leading to the persistence of the asymptomatic infections. To uncover these mechanisms, we aimed to identify parasite genetic factors implicated in asymptomatic infections through whole transcriptome analysis. We analyzed publicly available transcriptome datasets containing asymptomatic malaria (ASM), uncomplicated malaria (SM), and malaria-naïve (NSM) samples from 35 subjects for differentially expressed genes (DEGs) and long noncoding RNAs. Our analysis identified 755 and 1773 DEGs in ASM vs SM and NSM, respectively. These DEGs revealed sets of genes coding for proteins of unknown functions (PUFs) upregulated in ASM vs SM and ASM, suggesting their role in underlying fundamental molecular mechanisms during asymptomatic infections. Upregulated genes in ASM vs SM revealed a subset of 24 clonal variant genes (CVGs) involved in host-parasite and symbiotic interactions and modulation of the symbiont of host erythrocyte aggregation pathways. Moreover, we identified 237 differentially expressed noncoding RNAs in ASM vs SM, of which 11 were found to interact with CVGs, suggesting their possible role in regulating the expression of CVGs. Our results suggest that P. falciparum utilizes phenotypic plasticity as an adaptive mechanism during asymptomatic infections by upregulating clonal variant genes, with long noncoding RNAs possibly playing a crucial role in their regulation. Thus, our study provides insights into the parasites' genetic factors that confer a fitness advantage during asymptomatic infections.
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Affiliation(s)
- Joseph G. Amwoma
- Department of Biological Sciences, University of Embu, Kenya
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Sarah Kituyi
- Department of Biological Sciences, University of Embu, Kenya
- Forgarty International Center of the National Institutes of Health, Bethesda, MD, USA
| | - Dancan M. Wakoli
- Department of Biochemistry and Molecular Biology, Egerton University, Kenya
| | - Douglas O. Ochora
- Department of Biological Sciences, School of Pure and Applied Sciences, Kisii University, Kenya
- DSI/NWU, Preclinical Drug Development Platform, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Gladys Chemwor
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Risper Maisiba
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Winnie Okore
- Department of Biomedical Sciences and Technology, Maseno University, Kenya
| | - Benjamin Opot
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Dennis Juma
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Eric M.O. Muok
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Eric C. Garges
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | - Timothy E. Egbo
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Hoseah M. Akala
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
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47
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Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun 2024; 15:1724. [PMID: 38409232 PMCID: PMC10897432 DOI: 10.1038/s41467-024-46082-5] [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: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
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Affiliation(s)
- Benjamin J M Tremblay
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Cristina P Santini
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yajiao Cheng
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Xue Zhang
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
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48
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Zdyrski C, Gabriel V, Gessler TB, Ralston A, Sifuentes-Romero I, Kundu D, Honold S, Wickham H, Topping NE, Sahoo DK, Bista B, Tamplin J, Ospina O, Piñeyro P, Arriaga M, Galan JA, Meyerholz DK, Allenspach K, Mochel JP, Valenzuela N. Establishment and characterization of turtle liver organoids provides a potential model to decode their unique adaptations. Commun Biol 2024; 7:218. [PMID: 38388772 PMCID: PMC10883927 DOI: 10.1038/s42003-024-05818-1] [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: 09/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024] Open
Abstract
Painted turtles are remarkable for their freeze tolerance and supercooling ability along with their associated resilience to hypoxia/anoxia and oxidative stress, rendering them an ideal biomedical model for hypoxia-induced injuries (including strokes), tissue cooling during surgeries, and organ cryopreservation. Yet, such research is hindered by their seasonal reproduction and slow maturation. Here we developed and characterized adult stem cell-derived turtle liver organoids (3D self-assembled in vitro structures) from painted, snapping, and spiny softshell turtles spanning ~175My of evolution, with a subset cryopreserved. This development is, to the best of our knowledge, a first for this vertebrate Order, and complements the only other non-avian reptile organoids from snake venom glands. Preliminary characterization, including morphological, transcriptomic, and proteomic analyses, revealed organoids enriched in cholangiocytes. Deriving organoids from distant turtles and life stages demonstrates that our techniques are broadly applicable to chelonians, permitting the development of functional genomic tools currently lacking in herpetological research. Such platform could potentially support studies including genome-to-phenome mapping, gene function, genome architecture, and adaptive responses to climate change, with implications for ecological, evolutionary, and biomedical research.
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Affiliation(s)
- Christopher Zdyrski
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
- 3D Health Solutions Inc., Ames, IA, USA.
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA.
| | - Vojtech Gabriel
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Thea B Gessler
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Itzel Sifuentes-Romero
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Debosmita Kundu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Sydney Honold
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Hannah Wickham
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Nicholas E Topping
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | - Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Tamplin
- Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA
| | - Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Pablo Piñeyro
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA
| | - Marco Arriaga
- Department of Human Genetics, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Jacob A Galan
- Department of Human Genetics, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | | | - Karin Allenspach
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
- 3D Health Solutions Inc., Ames, IA, USA
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA
| | - Jonathan P Mochel
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
- 3D Health Solutions Inc., Ames, IA, USA
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
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49
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Hu J, Li S, Zhong X, Wei Y, Sun Q, Zhong L. Human umbilical cord mesenchymal stem cells attenuate diet-induced obesity and NASH-related fibrosis in mice. Heliyon 2024; 10:e25460. [PMID: 38356602 PMCID: PMC10864966 DOI: 10.1016/j.heliyon.2024.e25460] [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: 09/12/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a progressive form of non-alcoholic fatty liver disease (NAFLD) that may progress to cirrhosis and hepatocellular carcinoma but has no available treatment. Mesenchymal stem cells (MSCs) have become increasingly prominent in cell therapy. Human umbilical cord MSCs (hUC-MSCs) are considered superior to other MSCs due to their strong immunomodulatory ability, ease of collection, low immune rejection, and no tumorigenicity. Though hUC-MSCs have received increasing attention in research, they have been rarely applied in any investigations or treatments of NASH and associated fibrosis. Therefore, this study evaluated the therapeutic efficacy of hUC-MSCs in C57BL/6 mice with diet-induced NASH. At week 32, mice were randomized into two groups: phosphate-buffered saline and MSCs, which were injected into the tail vein. At week 40, glucose metabolism was evaluated using glucose and insulin tolerance tests. NASH-related indicators were examined using various biological methods. hUC-MSC administration alleviated obesity, glucose metabolism, hepatic steatosis, inflammation, and fibrosis. Liver RNA-seq showed that the expression of the acyl-CoA thioesterase (ACOT) family members Acot1, Acot2, and Acot3 involved in fatty acid metabolism were altered. The cytochrome P450 (CYP) members Cyp4a10 and Cyp4a14, which are involved in the peroxisome proliferator-activator receptor (PPAR) signaling pathway, were significantly downregulated after hUC-MSC treatment. In conclusion, hUC-MSCs effectively reduced Western diet-induced obesity, NASH, and fibrosis in mice, partly by regulating lipid metabolism and the PPAR signaling pathway.
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Affiliation(s)
- Jiali Hu
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shan Li
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuan Zhong
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yushuang Wei
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China
| | - Qinjuan Sun
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lan Zhong
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China
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50
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Shibata T, Shimoda M, Kobayashi T, Arai H, Owashi Y, Uehara T. High-quality genome of the zoophytophagous stink bug, Nesidiocoris tenuis, informs their food habit adaptation. G3 (BETHESDA, MD.) 2024; 14:jkad289. [PMID: 38113473 PMCID: PMC10849345 DOI: 10.1093/g3journal/jkad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 09/21/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
The zoophytophagous stink bug, Nesidiocoris tenuis, is a promising natural enemy of micro-pests such as whiteflies and thrips. This bug possesses both phytophagous and entomophagous food habits, enabling it to obtain nutrition from both plants and insects. This trait allows us to maintain its population density in agricultural fields by introducing insectary plants, even when the pest prey density is extremely low. However, if the bugs' population becomes too dense, they can sometimes damage crop plants. This dual character seems to arise from the food preferences and chemosensation of this predator. To understand the genomic landscape of N. tenuis, we examined the whole genome sequence of a commercially available Japanese strain. We used long-read sequencing and Hi-C analysis to assemble the genome at the chromosomal level. We then conducted a comparative analysis of the genome with previously reported genomes of phytophagous and hematophagous stink bugs to focus on the genetic factors contributing to this species' herbivorous and carnivorous tendencies. Our findings suggest that the gustatory gene set plays a pivotal role in adapting to food habits, making it a promising target for selective breeding. Furthermore, we identified the whole genomes of microorganisms symbiotic with this species through genomic analysis. We believe that our results shed light on the food habit adaptations of N. tenuis and will accelerate breeding efforts based on new breeding techniques for natural enemy insects, including genomics and genome editing.
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Affiliation(s)
- Tomofumi Shibata
- Division of Insect Advanced Technology, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masami Shimoda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tetsuya Kobayashi
- Division of Insect Advanced Technology, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroshi Arai
- Division of Insect Advanced Technology, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Yuta Owashi
- Division of Insect Advanced Technology, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Takuya Uehara
- Division of Insect Advanced Technology, Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
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