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Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ. The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L. BMC PLANT BIOLOGY 2024; 24:601. [PMID: 38926852 PMCID: PMC11201900 DOI: 10.1186/s12870-024-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/19/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RESULTS We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues. CONCLUSION The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
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Affiliation(s)
- Evelyn Kulesza
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Patrick Thomas
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah F Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- USDA Animal and Plant Health Inspection Service (APHIS), Riverdale, MD, 20737, USA
| | - Akiva Shalit-Kaneh
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Plant Sciences, Volcani-ARO (Agricultural and Rural Organization), Gilat, Israel
| | - Eric Wafula
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Benjamin Knollenberg
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Mars Inc, Davis, CA, 95616, USA
| | - Noah Winters
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Eddi Esteban
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Craig Praul
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lena Landherr
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude dePamphilis
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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Secci-Petretto G, Weiss S, Gomes-Dos-Santos A, Persat H, Machado AM, Vasconcelos I, Castro LFC, Froufe E. A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus. Genetica 2024; 152:71-81. [PMID: 38888686 PMCID: PMC11199216 DOI: 10.1007/s10709-024-00210-7] [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: 01/15/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.
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Affiliation(s)
- Giulia Secci-Petretto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Steven Weiss
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - Henri Persat
- Société Française d'Ichthyologie, Muséum National d'Histoire Naturelle Paris, France, 57 Rue Cuvier CP26, 75005, Paris, France
| | - André M Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Inês Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
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Connell ML, Meyer DN, Haimbaugh A, Baker TR. Status of single-cell RNA sequencing for reproductive toxicology in zebrafish and the transcriptomic trade-off. CURRENT OPINION IN TOXICOLOGY 2024; 38:100463. [PMID: 38846809 PMCID: PMC11155726 DOI: 10.1016/j.cotox.2024.100463] [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] [Indexed: 06/09/2024]
Abstract
The utilization of transcriptomic studies identifying profiles of gene expression, especially in toxicogenomics, has catapulted next-generation sequencing to the forefront of reproductive toxicology. An innovative yet underutilized RNA sequencing technique emerging into this field is single-cell RNA sequencing (scRNA-seq), which provides sequencing at the individual cellular level of gonad tissue. ScRNA-seq provides a novel and unique perspective for identifying distinct cellular profiles, including identification of rare cell subtypes. The specificity of scRNA-seq is a powerful tool for reproductive toxicity research, especially for translational animal models including zebrafish. Studies to date not only have focused on 'tissue atlassing' or characterizing what cell types make up different tissues but have also begun to include toxicant exposure as a factor that this review aims to explore. Future scRNA-seq studies will contribute to understanding exposure-induced outcomes; however, the trade-offs with traditional methods need to be considered.
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Affiliation(s)
- Mackenzie L Connell
- University of Florida, Department of Environmental & Global Health, 2173 Mowry Rd, Gainesville, FL 32611, USA
| | - Danielle N Meyer
- University of Florida, Department of Environmental & Global Health, 2173 Mowry Rd, Gainesville, FL 32611, USA
| | - Alex Haimbaugh
- University of Florida, Department of Environmental & Global Health, 2173 Mowry Rd, Gainesville, FL 32611, USA
| | - Tracie R Baker
- University of Florida, Department of Environmental & Global Health, 2173 Mowry Rd, Gainesville, FL 32611, USA
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Liu P, Li Z, Zhang Q, Qiao J, Zheng C, Zheng W, Zhang H. Identification of testis development-related genes by combining Iso-Seq and RNA-Seq in Zeugodacus tau. Front Cell Dev Biol 2024; 12:1356151. [PMID: 38529408 PMCID: PMC10961823 DOI: 10.3389/fcell.2024.1356151] [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: 12/15/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction: Zeugodacus tau (Walker) is an invasive pest. An effective method to control this pest is the sterile insect technique (SIT). To better apply this technique, it is necessary to understand testis development progression. Methods: Differentially expressed genes (DEGs) during testis development were analyzed by PacBio Iso-Seq and RNA-seq. Results: RNA-Seq library of Z. tau testes on day 1, 6, and 11 post eclosion were constructed. We identified 755 and 865 differentially expressed genes in the comparisons of T6 (testes on day 6) vs. T1 and T11 vs. T1, respectively. The KEGG pathway analysis showed that the DEGs were significantly enriched in retinol metabolism, vitamin B6 metabolism, and ascorbate and aldarate metabolism pathways. Knockdown of retinol dehydrogenase 12-like (rdh12-like), pyridoxal kinase (pdxk) and regucalcin (rgn), the representative gene in each of the above 3 pathways, reduced the hatching rate of Z. tau offspring. In addition, we identified 107 Drosophila spermatogenesis-related orthologous genes in Z. tau, of which innexin 2 (inx2) exhibited significantly up-regulated expression throughout testis development, and the knockdown of this gene reduced offspring hatching rate. Discussion: Our data indicated that rdh12-like, pdxk, rgn, and inx2 genes were related to testis development, and they were conserved in tephritid species. These results suggested that this gene might have the same function in tephritid. The findings provide an insight into testis development and spermatogenesis in tephritid species.
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Affiliation(s)
- Peipei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ziniu Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiuyuan Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiao Qiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chenjun Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wenping Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hongyu Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- China-Australia Joint Research Centre for Horticultural and Urban Pests, Huazhong Agricultural University, Wuhan, Hubei, China
- Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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Wu M, Zhang Y, Guo P, Liu H, Xia L, Wang M, Zeng C, Wang H, Shang F. Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight into Molecular Mechanisms of Flavonoid Metabolites Biosynthesis in Styphnolobium japonicum. Genes (Basel) 2024; 15:329. [PMID: 38540388 PMCID: PMC10970609 DOI: 10.3390/genes15030329] [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: 02/03/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Styphnolobium japonicum L. is a commonly consumed plant in China, known for its medicinal and nutritional benefits. This study focuses on the medicinal properties influenced by flavonoid metabolites, which vary during flower development. Utilizing full-length transcriptome sequencing on S. japonicum flowers, we observed changes in gene expression levels as the flowers progressed through growth stages. During stages S1 and S2, key genes related to flavonoid synthesis (PAL, 4CL, CHS, F3H, etc.) exhibited heightened expression. A weighted gene co-expression network analysis (WGCNA) identified regulatory genes (MYB, bHLH, WRKY) potentially involved in the regulatory network with flavonoid biosynthesis-related genes. Our findings propose a regulatory mechanism for flavonoid synthesis in S. japonicum flowers, elucidating the genetic underpinnings of this process. The identified candidate genes present opportunities for genetic enhancements in S. japonicum, offering insights into potential applications for improving its medicinal attributes.
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Affiliation(s)
- Miao Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Yu Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Peng Guo
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Huiyuan Liu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Linkui Xia
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Mengyuan Wang
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Chuqi Zeng
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Hongwei Wang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Fude Shang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
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Xu F, Liu S, Zhao A, Shang M, Wang Q, Jiang S, Cheng Q, Chen X, Zhai X, Zhang J, Wang X, Yan J. iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. THE NEW PHYTOLOGIST 2024; 241:2606-2620. [PMID: 38291701 DOI: 10.1111/nph.19554] [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: 10/24/2023] [Accepted: 01/06/2024] [Indexed: 02/01/2024]
Abstract
The advent of full-length transcriptome sequencing technologies has accelerated the discovery of novel splicing isoforms. However, existing alternative splicing (AS) tools are either tailored for short-read RNA-Seq data or designed for human and animal studies. The disparities in AS patterns between plants and animals still pose a challenge to the reliable identification and functional exploration of novel isoforms in plants. Here, we developed integrated full-length alternative splicing analysis (iFLAS), a plant-optimized AS toolkit that introduced a semi-supervised machine learning method known as positive-unlabeled (PU) learning to accurately identify novel isoforms. iFLAS also enables the investigation of AS functions from various perspectives, such as differential AS, poly(A) tail length, and allele-specific AS (ASAS) analyses. By applying iFLAS to three full-length transcriptome sequencing datasets, we systematically identified and functionally characterized maize (Zea mays) AS patterns. We found intron retention not only introduces premature termination codons, resulting in lower expression levels of isoforms, but may also regulate the length of 3'UTR and poly(A) tail, thereby affecting the functional differentiation of isoforms. Moreover, we observed distinct ASAS patterns in two genes within heterosis offspring, highlighting their potential value in breeding. These results underscore the broad applicability of iFLAS in plant full-length transcriptome-based AS research.
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Affiliation(s)
- Feng Xu
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Songyu Liu
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Anwen Zhao
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Meiqi Shang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Qian Wang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Shuqin Jiang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Qian Cheng
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Xingming Chen
- Molbreeding Biotechnology Co., Ltd, Shijiazhuang, Hebei Province, 051430, China
| | - Xiaoguang Zhai
- Molbreeding Biotechnology Co., Ltd, Shijiazhuang, Hebei Province, 051430, China
| | - Jianan Zhang
- Molbreeding Biotechnology Co., Ltd, Shijiazhuang, Hebei Province, 051430, China
| | - Xiangfeng Wang
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Jun Yan
- State Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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Zhu F, Lu J, Sun K, Deng C, Xu Y. Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing. BMC Genom Data 2024; 25:23. [PMID: 38408920 PMCID: PMC10895795 DOI: 10.1186/s12863-024-01208-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: 03/03/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates. METHODS In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species. RESULTS A total of 51,849 nonredundant full-length transcript assemblies (with an N50 length of 2980 bp) from I. braminus were generated and fully annotated using various gene function databases. Our analysis provides preliminary evidence supporting a recent genome duplication event in I. braminus. Phylogenetic analysis indicated that the divergence of I. braminus subgenomes occurred approximately 11.5 ~ 15 million years ago (Mya). The full-length transcript resource generated as part of this research will facilitate transcriptome analysis and genomic evolution studies in the future.
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Affiliation(s)
- Fei Zhu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China.
| | - Jing Lu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Ke Sun
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, 610000, Chengdu, China
| | - Yu Xu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
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Peng Y, Wang Z, Li M, Wang T, Su Y. Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns. BMC PLANT BIOLOGY 2024; 24:73. [PMID: 38273309 PMCID: PMC10811885 DOI: 10.1186/s12870-024-04746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. RESULTS In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. CONCLUSIONS Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.
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Affiliation(s)
- Yang Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ting Wang
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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9
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Liao T, Zhang L, Wang Y, Guo L, Cao J, Liu G. Full-length transcriptome characterization of Platycladus orientalis based on the PacBio platform. Front Genet 2024; 15:1345039. [PMID: 38304337 PMCID: PMC10830785 DOI: 10.3389/fgene.2024.1345039] [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: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
As a unique and native conifer in China, Platycladus orientalis is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of P. orientalis and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of P. orientalis offer a pioneering insight for future investigations into gene function and genetic breeding within Platycladus species.
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Affiliation(s)
| | | | | | | | | | - Guobin Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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10
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Titarenko V, Titarenko S. PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches. BMC Bioinformatics 2023; 24:396. [PMID: 37875804 PMCID: PMC10594774 DOI: 10.1186/s12859-023-05517-4] [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: 11/04/2021] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candidate positions within a reference sequence. We may create pairs ("position", "subsequence") for the reference sequence and keep all such records without compression, even on a budget computer. As sequences for new and reference genomes differ, the goal is to find anchors, so we tolerate differences and keep the number of candidate positions with the same anchors to a minimum. Spaced seeds (masks ignoring symbols at specific locations) are a way to approach the task. An ideal (full sensitivity) spaced seed should enable us to find all such positions subject to a given maximum number of mismatches permitted. RESULTS Several algorithms to assist seed generation are presented. The first one finds all permitted spaced seeds iteratively. We observe specific patterns for the seeds of the highest weight. There are often periodic seeds with a simple relation between block size, length of the seed and read. The second algorithm produces blocks for periodic seeds for blocks of up to 50 symbols and up to nine mismatches. The third algorithm uses those lists to find spaced seeds for reads of an arbitrary length. Finally, we apply seeds to a real dataset and compare results for other popular seeds. CONCLUSIONS PerFSeeB approach helps to significantly reduce the number of reads' possible alignment positions for a known number of mismatches. Lists of long, high-weight spaced seeds are available in Additional file 1. The seeds are best in weight compared to seeds from other papers and can usually be applied to shorter reads. Codes for all algorithms and periodic blocks can be found at https://github.com/vtman/PerFSeeB .
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Affiliation(s)
- Valeriy Titarenko
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Sofya Titarenko
- School of Mathematics, University of Leeds, Woodhouse, Leeds, LS2 9JT, UK
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11
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de Koning W, Feenstra FF, Calkoen FGJ, van der Lugt J, Kester LA, Mustafa DAM. Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing. Cancer Immunol Immunother 2023; 72:2659-2670. [PMID: 37072536 PMCID: PMC10361846 DOI: 10.1007/s00262-023-03450-2] [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: 11/23/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
BACKGROUND Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA sequencing for fresh frozen samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples. RESULTS Our results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In addition, both techniques showed that the immune landscape was heterogeneous in the 6 ependymoma samples used for this study. CONCLUSIONS The low-abundant genes were detected in higher quantities using the NanoString technique, even when FFPE samples were used. RNA sequencing is better suited for biomarker discovery, fusion gene detection, and getting a broader overview of the TIME. The technique that was used to measure the samples had a considerable effect on the type of immune cells that were identified. The limited number of tumor-infiltrating immune cells compared to the high density of tumor cells in ependymoma can limit the sensitivity of RNA expression techniques regarding the identification of the infiltrating immune cells.
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Affiliation(s)
- W. de Koning
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Clinical Bioinformatics Unit, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - F. F. Feenstra
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - F. G. J. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - J. van der Lugt
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - L. A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - D. A. M. Mustafa
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
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12
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Luo Y, Zhang Y, Le J, Li Q, Mou J, Deng S, Li J, Wang R, Deng Z, Liu J. Full-Length Transcriptome Sequencing Reveals the Molecular Mechanism of Metasequoia glyptostroboides Seed Responding to Aging. Antioxidants (Basel) 2023; 12:1353. [PMID: 37507893 PMCID: PMC10376015 DOI: 10.3390/antiox12071353] [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: 05/03/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Metasequoia glyptostroboides, Hu and W. C. Cheng, as the only surviving relict species of the Taxodiaceae Metasequoia genus, is a critically endangered and protected species in China. There is a risk of extinction due to the low vigor of M. glyptostroboides seeds, and the physiological mechanism of seed aging in M. glyptostroboides is not yet clear. In order to investigate the physiological and molecular mechanisms underlying the aging process of M. glyptostroboides seeds, we analyzed the antioxidant system and transcriptome at 0, 2, 4, 6, and 8 days after artificial accelerated aging treatment at 40 °C and 100% relative humidity. It was found that the germination percentage of fresh dried M. glyptostroboides seeds was 54 ± 5.29%, and significantly declined to 9.33 ± 1.88% after 6 days of aging, and then gradually decreased until the seed died on day 8. Superoxide dismutase (SOD) activity, ascorbic acid (AsA), glutathione (GSH) content and superoxide anion (O2·-) content and production rate significantly decreased, while malondialdehyde (MDA) and hydrogen peroxide (H2O2) content and glutathione peroxidase (GPX) and catalase (CAT) activity gradually increased during the aging process. A total of 42,189 unigenes were identified in the whole transcriptome, and 40,446 (95.86%) unigenes were annotated in at least one protein database. A total of 15,376 differentially expressed genes (DEGs) were obtained; KEGG enrichment analysis results revealed that seed aging may be mainly involved in the protein-processing pathways in endoplasmic reticulum, oxidative phosphorylation, and ascorbate and aldarate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the dark magenta, orange, and medium purple modules were highly correlated with physiological indicators such as SOD, CAT, and GSH and further identified 40 hub genes such as Rboh, ACO, HSF, and CML as playing important roles in the antioxidant network of M. glyptostroboides seeds. These findings provide a broader perspective for studying the regulatory mechanism of seed aging and a large number of potential target genes for the breeding of other endangered gymnosperms.
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Affiliation(s)
- Yongjian Luo
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Yixin Zhang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jingyu Le
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Qing Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jiaolin Mou
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Shiming Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Jitao Li
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Ru Wang
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization, Hubei Minzu University, Enshi 445000, China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture, Hubei Minzu University, Enshi 445000, China
- The Plant Germplasm Resources Laboratory, School of Forestry and Horticulture, Hubei Minzu University, Enshi 445000, China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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13
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Alqahtani T, Deore SL, Kide AA, Shende BA, Sharma R, Chakole RD, Nemade LS, Kale NK, Borah S, Deokar SS, Behera A, Dhawal Bhandari D, Gaikwad N, Azad AK, Ghosh A. Mitochondrial dysfunction and oxidative stress in Alzheimer's disease, and Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis -An updated review. Mitochondrion 2023:S1567-7249(23)00051-X. [PMID: 37269968 DOI: 10.1016/j.mito.2023.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Misfolded proteins in the central nervous system can induce oxidative damage, which can contribute to neurodegenerative diseases in the mitochondria. Neurodegenerative patients face early mitochondrial dysfunction, impacting energy utilization. Amyloid-ß and tau problems both have an effect on mitochondria, which leads to mitochondrial malfunction and, ultimately, the onset of Alzheimer's disease. Cellular oxygen interaction yields reactive oxygen species within mitochondria, initiating oxidative damage to mitochondrial constituents. Parkinson's disease, linked to oxidative stress, α-synuclein aggregation, and inflammation, results from reduced brain mitochondria activity. Mitochondrial dynamics profoundly influence cellular apoptosis via distinct causative mechanisms. The condition known as Huntington's disease is characterized by an expansion of polyglutamine, primarily impactingthe cerebral cortex and striatum. Research has identified mitochondrial failure as an early pathogenic mechanism contributing to HD's selective neurodegeneration. The mitochondria are organelles that exhibit dynamism by undergoing fragmentation and fusion processes to attain optimal bioenergetic efficiency. They can also be transported along microtubules and regulateintracellular calcium homeostasis through their interaction with the endoplasmic reticulum. Additionally, the mitochondria produce free radicals. The functions of eukaryotic cells, particularly in neurons, have significantly deviated from the traditionally assigned role of cellular energy production. Most of them areimpaired in HD, which may lead to neuronal dysfunction before symptoms manifest. This article summarises the most important changes in mitochondrial dynamics that come from neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and Amyotrophic Lateral Sclerosis. Finally, we discussed about novel techniques that can potentially treat mitochondrial malfunction and oxidative stress in four most dominating neuro disorders.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia.
| | | | | | | | - Ritika Sharma
- University institute of pharma sciences, Chandigarh University, Mohali, Punjab.
| | - Rita Dadarao Chakole
- Government College of Pharmacy Vidyanagar Karad Dist Satara Maharashtra Pin 415124.
| | - Lalita S Nemade
- Govindrao Nikam College of Pharmacy Sawarde Maharashtra 415606.
| | | | - Sudarshana Borah
- Department of Pharmacognosy, University of Science and Technology Meghalaya Technocity, Ri-Bhoi District Meghalaya.
| | | | - Ashok Behera
- Faculty of Pharmacy, DIT University, Dehradun,Uttarakhand.
| | - Divya Dhawal Bhandari
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014. India.
| | - Nikita Gaikwad
- Department of Pharmaceutics, P.E.S. Modern College of Pharmacy, Nigdi, Pune-411044.
| | - Abul Kalam Azad
- Faculty of Pharmacy MAHSA University Bandar Saujana putra, 42610, Selangor, Malaysia
| | - Arabinda Ghosh
- Department of Botany, Gauhati University, Guwahati, 781014, Assam, India
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14
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Dehghanzad R, Khalafiyan A, Khanahmad H. The Necessity of Using Strand-Specific cDNA for Achieving Accurate Transcriptome Analysis Result. Adv Biomed Res 2023; 12:108. [PMID: 37288031 PMCID: PMC10241614 DOI: 10.4103/abr.abr_102_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 06/09/2023] Open
Affiliation(s)
- Reyhaneh Dehghanzad
- Department of Medical Genetics, Faculty of Medical Science, Tehran University of Medical Science, Tehran, Iran
| | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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15
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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16
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Ray SK, Mukherjee S. Neuropharmacology of Alcohol Addiction with Special Emphasis on Proteomic Approaches for Identification of Novel Therapeutic Targets. Curr Neuropharmacol 2023; 21:119-132. [PMID: 35959616 PMCID: PMC10193758 DOI: 10.2174/1570159x20666220811092906] [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: 01/14/2022] [Revised: 07/01/2022] [Accepted: 07/10/2022] [Indexed: 02/04/2023] Open
Abstract
Alcohol is a generic pharmacological agent with only a few recognized primary targets. Nmethyl- D-aspartate, gamma-aminobutyric acid, glycine, 5-hydroxytryptamine 3 (serotonin), nicotinic acetylcholine receptors, and L-type Ca2+ channels and G-protein-activated inwardly rectifying K channels are all involved. Following the first hit of alcohol on specific brain targets, the second wave of indirect effects on various neurotransmitter/neuropeptide systems begins, leading to the typical acute behavioral effects of alcohol, which range from disinhibition to sedation and even hypnosis as alcohol concentrations rise. Recent research has revealed that gene regulation is significantly more complex than previously thought and does not fully explain changes in protein levels. As a result, studying the proteome directly, which differs from the genome/transcriptome in terms of complexity and dynamicity, has provided unique insights into extraordinary advances in proteomic techniques that have changed the way we can analyze the composition, regulation, and function of protein complexes and pathways underlying altered neurobiological conditions. Neuroproteomics has the potential to revolutionize alcohol research by allowing researchers to gain a better knowledge of how alcohol impacts protein structure, function, connections, and networks on a global scale. The amount of information collected from these breakthroughs can aid in identifying valuable biomarkers for early detection and improved prognosis of an alcohol use disorder and future pharmaceutical targets for the treatment of alcoholism.
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Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh 462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Science, Bhopal, Madhya Pradesh 462020, India
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17
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Guimaraes PM, Quintana AC, Mota APZ, Berbert PS, Ferreira DDS, de Aguiar MN, Pereira BM, de Araújo ACG, Brasileiro ACM. Engineering Resistance against Sclerotinia sclerotiorum Using a Truncated NLR (TNx) and a Defense-Priming Gene. PLANTS (BASEL, SWITZERLAND) 2022; 11:3483. [PMID: 36559595 PMCID: PMC9786959 DOI: 10.3390/plants11243483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The association of both cell-surface PRRs (Pattern Recognition Receptors) and intracellular receptor NLRs (Nucleotide-Binding Leucine-Rich Repeat) in engineered plants have the potential to activate strong defenses against a broad range of pathogens. Here, we describe the identification, characterization, and in planta functional analysis of a novel truncated NLR (TNx) gene from the wild species Arachis stenosperma (AsTIR19), with a protein structure lacking the C-terminal LRR (Leucine Rich Repeat) domain involved in pathogen perception. Overexpression of AsTIR19 in tobacco plants led to a significant reduction in infection caused by Sclerotinia sclerotiorum, with a further reduction in pyramid lines containing an expansin-like B gene (AdEXLB8) potentially involved in defense priming. Transcription analysis of tobacco transgenic lines revealed induction of hormone defense pathways (SA; JA-ET) and PRs (Pathogenesis-Related proteins) production. The strong upregulation of the respiratory burst oxidase homolog D (RbohD) gene in the pyramid lines suggests its central role in mediating immune responses in plants co-expressing the two transgenes, with reactive oxygen species (ROS) production enhanced by AdEXLB8 cues leading to stronger defense response. Here, we demonstrate that the association of potential priming elicitors and truncated NLRs can produce a synergistic effect on fungal resistance, constituting a promising strategy for improved, non-specific resistance to plant pathogens.
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Affiliation(s)
- Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
| | | | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, CNRS, Université Côte d’Azur, 06903 Sophia Antipolis, France
| | | | | | | | | | | | - Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
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18
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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19
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Maia GA, Filho VB, Kawagoe EK, Teixeira Soratto TA, Moreira RS, Grisard EC, Wagner G. AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data. Front Genet 2022; 13:1020100. [DOI: 10.3389/fgene.2022.1020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/11/2022] [Indexed: 11/23/2022] Open
Abstract
Assignment of gene function has been a crucial, laborious, and time-consuming step in genomics. Due to a variety of sequencing platforms that generates increasing amounts of data, manual annotation is no longer feasible. Thus, the need for an integrated, automated pipeline allowing the use of experimental data towards validation of in silico prediction of gene function is of utmost relevance. Here, we present a computational workflow named AnnotaPipeline that integrates distinct software and data types on a proteogenomic approach to annotate and validate predicted features in genomic sequences. Based on FASTA (i) nucleotide or (ii) protein sequences or (iii) structural annotation files (GFF3), users can input FASTQ RNA-seq data, MS/MS data from mzXML or similar formats, as the pipeline uses both transcriptomic and proteomic information to corroborate annotations and validate gene prediction, providing transcription and expression evidence for functional annotation. Reannotation of the available Arabidopsis thaliana, Caenorhabditis elegans, Candida albicans, Trypanosoma cruzi, and Trypanosoma rangeli genomes was performed using the AnnotaPipeline, resulting in a higher proportion of annotated proteins and a reduced proportion of hypothetical proteins when compared to the annotations publicly available for these organisms. AnnotaPipeline is a Unix-based pipeline developed using Python and is available at: https://github.com/bioinformatics-ufsc/AnnotaPipeline.
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20
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Correspondence: (M.K.T.); (N.T.)
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
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21
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Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development. Int J Mol Sci 2022; 23:ijms231911547. [PMID: 36232849 PMCID: PMC9569805 DOI: 10.3390/ijms231911547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.
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22
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Sheikh-Assadi M, Naderi R, Salami SA, Kafi M, Fatahi R, Shariati V, Martinelli F, Cicatelli A, Triassi M, Guarino F, Improta G, Claros MG. Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss. PLANTS 2022; 11:plants11182365. [PMID: 36145766 PMCID: PMC9503428 DOI: 10.3390/plants11182365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/21/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed and compared using 11 constructed transcriptomes. Concisely, normalized benchmarking demonstrated that Velvet–Oases suffer from the worst results, while the EvidentialGene strategy can provide the most comprehensive and accurate transcriptome of Lilium ledebourii (Baker) Boiss. The BLAST results also confirmed the superiority of EvidentialGene, so it could capture even up to 59% more (than Velvet–Oases) unique gene hits. To promote assembly optimization, with the help of normalized benchmarking, PCA and AHC, it is emphasized that each metric can only provide part of the transcriptome status, and one should never settle for just a few evaluation criteria. This study supplies a framework for benchmarking and optimizing the efficiency of assembly approaches to analyze RNA-Seq data and reveals that selecting an inefficient assembly strategy might result in less identification of unique gene hits.
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Affiliation(s)
- Morteza Sheikh-Assadi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj 31587-77871, Iran
- Correspondence: (M.S.-A.); (R.N.)
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj 31587-77871, Iran
- Correspondence: (M.S.-A.); (R.N.)
| | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj 31587-77871, Iran
| | - Mohsen Kafi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj 31587-77871, Iran
| | - Reza Fatahi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj 31587-77871, Iran
| | - Vahid Shariati
- NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran 14965/161, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy
| | - Maria Triassi
- Department of Public Health, University of Naples “Federico II”, 80131 Naples, Italy
| | - Francesco Guarino
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, 84084 Fisciano, Italy
| | - Giovanni Improta
- Department of Public Health, University of Naples “Federico II”, 80131 Naples, Italy
| | - Manuel Gonzalo Claros
- Molecular Biology and Biochemistry Department, University of Málaga, 29071 Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), 29071 Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), 29010 Málaga, Spain
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23
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The performance of lactic acid bacteria in silage production: a review of modern biotechnology for silage improvement. Microbiol Res 2022; 266:127212. [DOI: 10.1016/j.micres.2022.127212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022]
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24
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van Vliet EA, Hildebrand MS, Mills JD, Brennan GP, Eid T, Masino SA, Whittemore V, Bindila L, Wang KK, Patel M, Perucca P, Reid CA. A companion to the preclinical common data elements for genomics, transcriptomics, and epigenomics data in rodent epilepsy models. A report of the TASK3-WG4 omics working group of the ILAE/AES joint translational TASK force. Epilepsia Open 2022. [PMID: 35950645 DOI: 10.1002/epi4.12640] [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: 12/12/2021] [Accepted: 02/22/2022] [Indexed: 11/06/2022] Open
Abstract
The International League Against Epilepsy/American Epilepsy Society (ILAE/AES) Joint Translational Task Force established the TASK3 working groups to create common data elements (CDEs) for various preclinical epilepsy research disciplines. The aim of the CDEs is to improve the standardization of experimental designs across a range of epilepsy research-related methods. Here, we have generated CDE tables with key parameters and case report forms (CRFs) containing the essential contents of the study protocols for genomics, transcriptomics, and epigenomics in rodent models of epilepsy, with a specific focus on adult rats and mice. We discuss the important elements that need to be considered for genomics, transcriptomics, and epigenomics methodologies, providing a rationale for the parameters that should be collected. This is the first in a two-part series of omics papers with the second installment to cover proteomics, lipidomics, and metabolomics in adult rodents.
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Affiliation(s)
- Erwin A van Vliet
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Gary P Brennan
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tore Eid
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Susan A Masino
- Neuroscience Program and Psychology Department, Life Sciences Center, Trinity College, Hartford, Connecticut, USA
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Kevin K Wang
- Department of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, Florida, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
| | - Manisha Patel
- Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Austin Health, Heidelberg, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Christopher A Reid
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
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25
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States,Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Amy L. Non, Tatum S. Simonson,
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26
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Xiong Y, Yang J, Xiong Y, Zhao J, Liu L, Liu W, Sha L, Zhou J, You M, Li D, Lei X, Bai S, Ma X. Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera. FRONTIERS IN PLANT SCIENCE 2022; 13:959042. [PMID: 35958193 PMCID: PMC9358441 DOI: 10.3389/fpls.2022.959042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2023]
Abstract
As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5'-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.
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Affiliation(s)
- Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lin Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiqiong Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Jeon MJ, Roy NS, Choi BS, Oh JY, Kim YI, Park HY, Um T, Kim NS, Kim S, Choi IY. Identifying Terpenoid Biosynthesis Genes in Euphorbia maculata via Full-Length cDNA Sequencing. Molecules 2022; 27:molecules27144591. [PMID: 35889464 PMCID: PMC9316252 DOI: 10.3390/molecules27144591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
The annual herb Euphorbia maculata L. produces anti-inflammatory and biologically active substances such as triterpenoids, tannins, and polyphenols, and it is used in traditional Chinese medicine. Of these bioactive compounds, terpenoids, also called isoprenoids, are major secondary metabolites in E. maculata. Full-length cDNA sequencing was carried out to characterize the transcripts of terpenoid biosynthesis reference genes and determine the copy numbers of their isoforms using PacBio SMRT sequencing technology. The Illumina short-read sequencing platform was also employed to identify differentially expressed genes (DEGs) in the secondary metabolite pathways from leaves, roots, and stems. PacBio generated 62 million polymerase reads, resulting in 81,433 high-quality reads. From these high-quality reads, we reconstructed a genome of 20,722 genes, in which 20,246 genes (97.8%) did not have paralogs. About 33% of the identified genes had two or more isoforms. DEG analysis revealed that the expression level differed among gene paralogs in the leaf, stem, and root. Whole sets of paralogs and isoforms were identified in the mevalonic acid (MVA), methylerythritol phosphate (MEP), and terpenoid biosynthesis pathways in the E. maculata L. The nucleotide information will be useful for identifying orthologous genes in other terpenoid-producing medicinal plants.
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Affiliation(s)
- Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
| | - Neha Samir Roy
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
| | | | - Ji Yeon Oh
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
| | - Yong-In Kim
- On Biological Resource Research Institute, Chuncheon 24239, Korea;
| | - Hye Yoon Park
- Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
| | - Nam-Soo Kim
- BIT Institute, NBIT Co., Ltd., Chuncheon 24341, Korea;
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
| | - Soonok Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
| | - Ik-Young Choi
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
- BIT Institute, NBIT Co., Ltd., Chuncheon 24341, Korea;
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
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Ye S, Yu X, Chen H, Zhang Y, Wu Q, Tan H, Song J, Saqib HSA, Farhadi A, Ikhwanuddin M, Ma H. Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂). BIOLOGY 2022; 11:biology11071026. [PMID: 36101407 PMCID: PMC9312322 DOI: 10.3390/biology11071026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary The eyestalk is a key organ in crustaceans that produces neurohormones and regulates a range of physiological functions. Eyestalk displacement was discovered in some first-generation (F1) offspring of the novel interspecific hybrid crab (Scylla serrata ♀ × S. paramamosain ♂). To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, high-quality transcriptome was reconstructed using single-molecule real-time (SMRT) sequencing. A total of 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in hybrid crabs with displaced eyestalks (DH). The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant gene ontology (GO) terms were related to the cuticle or chitin. Overall, this study highlights the underlying genetic mechanisms of eyestalk displacement and provide useful knowledge for mud crab (Scylla spp.) crossbreeding. Abstract The lack of high-quality juvenile crabs is the greatest impediment to the growth of the mud crab (Scylla paramamosain) industry. To obtain high-quality hybrid offspring, a novel hybrid mud crab (S. serrata ♀ × S. paramamosain ♂) was successfully produced in our previous study. Meanwhile, an interesting phenomenon was discovered, that some first-generation (F1) hybrid offspring’s eyestalks were displaced during the crablet stage I. To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, both single-molecule real-time (SMRT) and Illumina RNA sequencing were implemented. Using a two-step collapsing strategy, three high-quality reconstructed transcriptomes were obtained from purebred mud crabs (S. paramamosain) with normal eyestalks (SPA), hybrid crabs with normal eyestalks (NH), and hybrid crabs with displaced eyestalks (DH). In total, 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in DH. The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant GO terms were related to the cuticle or chitin. Overall, high-quality reconstructed transcriptomes were obtained for the novel interspecific hybrid crab and provided valuable insights into the genetic mechanisms of eyestalk displacement in mud crab (Scylla spp.) crossbreeding.
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Affiliation(s)
- Shaopan Ye
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Xiaoyan Yu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Huiying Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Qingyang Wu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Jun Song
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Hafiz Sohaib Ahmed Saqib
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Ardavan Farhadi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China; (S.Y.); (X.Y.); (H.C.); (Y.Z.); (Q.W.); (H.T.); (J.S.); (H.S.A.S.); (A.F.)
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China;
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
- Correspondence: ; Tel.: +86-754-86503471
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Hasan S, Huang L, Liu Q, Perlo V, O’Keeffe A, Margarido GRA, Furtado A, Henry RJ. The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts. RICE (NEW YORK, N.Y.) 2022; 15:29. [PMID: 35689714 PMCID: PMC9188635 DOI: 10.1186/s12284-022-00577-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/26/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome. RESULTS A cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel. CONCLUSION The data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.
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Affiliation(s)
- Sharmin Hasan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
- Department of Botany, Jagannath University, Dhaka, 1100 Bangladesh
| | - Lichun Huang
- College of Agriculture, Yangzhou University, Jiangsu, 225009 China
| | - Qiaoquan Liu
- College of Agriculture, Yangzhou University, Jiangsu, 225009 China
| | - Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
| | - Angela O’Keeffe
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072 Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072 Australia
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Liu T, Liu Y, Fu G, Chen J, Lv T, Su D, Wang Y, Hu X, Su X, Harris AJ. Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153630. [PMID: 35193087 DOI: 10.1016/j.jplph.2022.153630] [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: 10/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.
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Affiliation(s)
- Tao Liu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yuping Liu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Gui Fu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Jinyuan Chen
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Ting Lv
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Dandan Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yanan Wang
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xiayu Hu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Academy of Plateau Science and Sustainability, Xueyuan Road, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, Qinghai Normal University, No. 38 Wusixi Road, Xining, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Full-Length Transcriptome Characterization and Comparative Analysis of Chosenia arbutifolia. FORESTS 2022. [DOI: 10.3390/f13040543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As a unique tree species in the Salicaceae family, Chosenia arbutifolia is used primarily for construction materials and landscape planting in China. Compared with other Salicaceae species members, the genomic resources of C. arbutifolia are extremely scarce. Thus, in the present study, the full-length transcriptome of C. arbutifolia was sequenced by single-molecular real-time sequencing (SMRT) technology based on the PacBio platform. Then, it was compared against those of other Salicaceae species. We generated 17,397,064 subreads and 95,940 polished reads with an average length of 1812 bp, which were acquired through calibration, clustering, and polishing. In total, 50,073 genes were reconstructed, of which 48,174 open reading frames, 4281 long non-coding RNAs, and 3121 transcription factors were discovered. Functional annotation revealed that 47,717 genes had a hit in at least one of five reference databases. Moreover, a set of 12,332 putative SSR markers were screened among the reconstructed genes. Single-copy and special orthogroups, and divergent and conserved genes, were identified and analyzed to find divergence among C. arbutifolia and the five Salicaceae species. To reveal genes involved in a specific function and pathway, enrichment analyses for GO and KEGG were also performed. In conclusion, the present study empirically confirmed that SMRT sequencing realistically depicted the C. arbutifolia transcriptome and provided a comprehensive reference for functional genomic research on Salicaceae species.
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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RNA sequencing and its applications in cancer and rare diseases. Mol Biol Rep 2022; 49:2325-2333. [PMID: 34988891 PMCID: PMC8731134 DOI: 10.1007/s11033-021-06963-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022]
Abstract
With the invention of RNA sequencing over a decade ago, diagnosis and identification of the gene-related diseases entered a new phase that enabled more accurate analysis of the diseases that are difficult to approach and analyze. RNA sequencing has availed in-depth study of transcriptomes in different species and provided better understanding of rare diseases and taxonomical classifications of various eukaryotic organisms. Development of single-cell, short-read, long-read and direct RNA sequencing using both blood and biopsy specimens of the organism together with recent advancement in computational analysis programs has made the medical professional’s ability in identifying the origin and cause of genetic disorders indispensable. Altogether, such advantages have evolved the treatment design since RNA sequencing can detect the resistant genes against the existing therapies and help medical professions to take a further step in improving methods of treatments towards higher effectiveness and less side effects. Therefore, it is of essence to all researchers and scientists to have deeper insight in all available methods of RNA sequencing while taking a step-in therapy design.
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Kushwaha S, Mukherjee S, Chowdhury R, Chowdhury S. Analysis of Transcriptomic Data Generated from Drug-Treated Cancer Cell Line. Methods Mol Biol 2022; 2535:119-129. [PMID: 35867227 DOI: 10.1007/978-1-0716-2513-2_10] [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: 06/15/2023]
Abstract
Resistance to chemotherapy is one major obstacle in current cancer treatment. Therefore, understanding the molecular basis of the acquisition of resistance is vital for the design and development of appropriate cancer therapy. Importantly, acquisition of resistance is not a single-step process, and the molecular signature of cells dynamically changes during this process. With the advent of next-generation omic technologies, today one can precisely map the molecular alterations not only in a population of tumor cells but also at the single-cell level as they attain chemo-resistance. In this chapter, we describe a detailed transcriptomic pipeline following next-generation sequencing for mapping alteration in expression during the process of attainment of resistance. We provide comprehensive information on the process to (1) track the differential expression of transcripts, (2) understand the gene ontology functions, (3) filter out candidate key genes, (4) identify the pathways regulated by them, and (5) generate a map of their probable interactions. We assume that our analytical method will be useful for research in this direction.
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Affiliation(s)
- Swarnima Kushwaha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Sudeshna Mukherjee
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Rajdeep Chowdhury
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Shibasish Chowdhury
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
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35
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Yow AG, Bostan H, Castanera R, Ruggieri V, Mengist MF, Curaba J, Young R, Gillitt N, Iorizzo M. Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family. Genes (Basel) 2021; 13:genes13010052. [PMID: 35052394 PMCID: PMC8774480 DOI: 10.3390/genes13010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.
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Affiliation(s)
- Ashley G. Yow
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain;
| | | | - Molla F. Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
| | - Roberto Young
- Research Department of Dole, Standard Fruit de Honduras, Zona Mazapan, La Ceiba 31101, Honduras;
| | - Nicholas Gillitt
- Core Genomics Lab, David H. Murdock Research Institute, Kannapolis, NC 28081, USA;
| | - Massimo Iorizzo
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA; (H.B.); (M.F.M.); (J.C.)
- Correspondence:
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Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 2021; 37:110022. [PMID: 34788620 PMCID: PMC8609283 DOI: 10.1016/j.celrep.2021.110022] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/30/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community. There is widespread transcript diversity in the cortex and many novel transcripts Some genes display big differences in isoform number between human and mouse cortex There is evidence of differential transcript usage between human fetal and adult cortex There are many novel isoforms of genes associated with human brain disease
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Key Words
- isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing
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Affiliation(s)
| | | | - Isabel Castanho
- University of Exeter, Exeter, UK; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Connor Jops
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
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Rincón-Riveros A, Morales D, Rodríguez JA, Villegas VE, López-Kleine L. Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions. Int J Mol Sci 2021; 22:11397. [PMID: 34768830 PMCID: PMC8583695 DOI: 10.3390/ijms222111397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.
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Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia;
| | - Duvan Morales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Josefa Antonia Rodríguez
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá 111221, Colombia;
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Liliana López-Kleine
- Department of Statistics, Faculty of Science, Universidad Nacional de Colombia, Bogotá 111221, Colombia
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Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. Animals (Basel) 2021; 11:ani11102906. [PMID: 34679927 PMCID: PMC8532877 DOI: 10.3390/ani11102906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 02/06/2023] Open
Abstract
Domestic goats are commonly reared for meat and milk production in several regions of the world. However, the genetic mechanism underlying muscle development and meat quality of goats is limited. Therefore, the aim of this study was to identify known and novel genes regulating muscle development and meat quality of goats using second- and third-generation sequencing technologies. To achieve this, the meat quality and transcriptomes of longissimus dorsi (LD) and biceps femoris (BF) muscle tissues of Lingqiu Greyback goats were examined and compared. Differentially expressed genes (DEGs) and isoforms (DEIs) were functionally annotated. Results showed that 45,574 full-length transcripts covering 18,491 loci were characterized, and 12,566 genes were co-expressed in all samples. Differential expression analysis identified 231 DEGs, including 45 novel genes in the LD and BF muscles of the goats. Additionally, 1173 DEIs were found, in which 642 novel isoforms were identified in this study. Functional annotation and pathway analysis of the DEGs and DEIs revealed that some of them were associated with muscle growth and lipid metabolism. Overall, the findings of this study contribute to the understanding of the transcriptomic diversity underlying meat quality and muscle development of goat.
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Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus. Int J Mol Sci 2021; 22:ijms22179246. [PMID: 34502153 PMCID: PMC8431428 DOI: 10.3390/ijms22179246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/12/2023] Open
Abstract
Despite heterosis contributing to genetic improvements in crops, root growth heterosis in rapeseed plants is poorly understood at the molecular level. The current study was performed to discover key differentially expressed genes (DEGs) related to heterosis in two hybrids with contrasting root growth performance (FO; high hybrid and FV; low hybrid) based on analysis of the root heterosis effect. Based on comparative transcriptomic analysis, we believe that the overdominance at the gene expression level plays a critical role in hybrid roots’ early biomass heterosis. Our findings imply that a considerable increase in up-regulation of gene expression underpins heterosis. In the FO hybrid, high expression of DEGs overdominant in the starch/sucrose and galactose metabolic pathways revealed a link between hybrid vigor and root growth. DEGs linked to auxin, cytokinin, brassinosteroids, ethylene, and abscisic acid were also specified, showing that these hormones may enhance mechanisms of root growth and the development in the FO hybrid. Moreover, transcription factors such as MYB, ERF, bHLH, NAC, bZIP, and WRKY are thought to control downstream genes involved in root growth. Overall, this is the first study to provide a better understanding related to the regulation of the molecular mechanism of heterosis, which assists in rapeseed growth and yield improvement.
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Williams AM, Itgen MW, Broz AK, Carter OG, Sloan DB. Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora. G3 (BETHESDA, MD.) 2021; 11:jkab189. [PMID: 34849814 PMCID: PMC8496259 DOI: 10.1093/g3journal/jkab189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.
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Affiliation(s)
- Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olivia G Carter
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in Berberis koreana. PLANTS 2021; 10:plants10071314. [PMID: 34203474 PMCID: PMC8308982 DOI: 10.3390/plants10071314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022]
Abstract
Berberis koreana is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth. This was followed by full-length cDNA sequencing analysis using the PacBio sequencer platform to determine the number of isoforms of those expressed genes. We identified 23,246 full-length unigenes, among which 8479 had more than one isoform. The number of isoforms ranged between two to thirty-one among all genes. Complete isoform analysis was carried out on the unigenes encoding BIA synthesis. Thirteen of the sixteen genes encoding enzymes for berberine synthesis were present in more than one copy. This demonstrates that gene duplication and translation into isoforms may contribute to the functional specificity of the duplicated genes and isoforms in plant alkaloid synthesis. Our study also demonstrated the streamlining of berberine biosynthesis via the absence of genes for enzymes of other BIAs, but the presence of all the genes for berberine biosynthesize in B. koreana. In addition to genes encoding enzymes for the berberine biosynthesis pathway, the genes encoding enzymes for other BIAs were not present in our dataset except for those encoding corytuberine synthase (CTS) and berbamunine synthase (BS). Therefore, this explains how B. koreana produces berberine by blocking the pathways leading to other BIAs, effectively only allowing the pathway to lead to berberine synthesis.
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Yan H, Zhou H, Luo H, Fan Y, Zhou Z, Chen R, Luo T, Li X, Liu X, Li Y, Qiu L, Wu J. Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development. BMC PLANT BIOLOGY 2021; 21:228. [PMID: 34022806 PMCID: PMC8140441 DOI: 10.1186/s12870-021-02989-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/27/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. RESULTS Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. CONCLUSIONS Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.
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Affiliation(s)
- Haifeng Yan
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Hanmin Luo
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Zhongfeng Zhou
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Ting Luo
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Xujuan Li
- Sugarcane Research Institute of Yunnan Academy of Agricultural Sciences, East Lingquan Road 172, Kaiyun, 661600, Yunnan, China
| | - Xinlong Liu
- Sugarcane Research Institute of Yunnan Academy of Agricultural Sciences, East Lingquan Road 172, Kaiyun, 661600, Yunnan, China
| | - Yangrui Li
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Lihang Qiu
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China.
| | - Jianming Wu
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China.
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Navale V, Vamkudoth KR, Ajmera S, Dhuri V. Aspergillus derived mycotoxins in food and the environment: Prevalence, detection, and toxicity. Toxicol Rep 2021; 8:1008-1030. [PMID: 34408970 PMCID: PMC8363598 DOI: 10.1016/j.toxrep.2021.04.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Aspergillus species are the paramount ubiquitous fungi that contaminate various food substrates and produce biochemicals known as mycotoxins. Aflatoxins (AFTs), ochratoxin A (OTA), patulin (PAT), citrinin (CIT), aflatrem (AT), secalonic acids (SA), cyclopiazonic acid (CPA), terrein (TR), sterigmatocystin (ST) and gliotoxin (GT), and other toxins produced by species of Aspergillus plays a major role in food and human health. Mycotoxins exhibited wide range of toxicity to the humans and animal models even at nanomolar (nM) concentration. Consumption of detrimental mycotoxins adulterated foodstuffs affects human and animal health even trace amounts. Bioaerosols consisting of spores and hyphal fragments are active elicitors of bronchial irritation and allergy, and challenging to the public health. Aspergillus is the furthermost predominant environmental contaminant unswervingly defile lives with a 40-90 % mortality risk in patients with conceded immunity. Genomics, proteomics, transcriptomics, and metabolomics approaches useful for mycotoxins' detection which are expensive. Antibody based detection of toxins chemotypes may result in cross-reactivity and uncertainty. Aptamers (APT) are single stranded DNA (ssDNA/RNA), are specifically binds to the target molecules can be generated by systematic evolution of ligands through exponential enrichment (SELEX). APT are fast, sensitive, simple, in-expensive, and field-deployable rapid point of care (POC) detection of toxins, and a better alternative to antibodies.
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Affiliation(s)
- Vishwambar Navale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Koteswara Rao Vamkudoth
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | | | - Vaibhavi Dhuri
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
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Vichi J, Salazar E, Jacinto VJ, Rodriguez LO, Grande R, Dantán-González E, Morett E, Hernández-Mendoza A. High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth. PLoS One 2021; 16:e0248513. [PMID: 33730068 PMCID: PMC7968713 DOI: 10.1371/journal.pone.0248513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
In spite of increased complexity in eukaryotes compared to prokaryotes, several basic metabolic and regulatory processes are conserved. Here we explored analogies in the eubacteria Escherichia coli and the unicellular fission yeast Schizosaccharomyces pombe transcriptomes under two carbon sources: 2% glucose; or a mix of 2% glycerol and 0.2% sodium acetate using the same growth media and growth phase. Overall, twelve RNA-seq libraries were constructed. A total of 593 and 860 genes were detected as differentially expressed for E. coli and S. pombe, respectively, with a log2 of the Fold Change ≥ 1 and False Discovery Rate ≤ 0.05. In aerobic glycolysis, most of the expressed genes were associated with cell proliferation in both organisms, including amino acid metabolism and glycolysis. In contrast in glycerol/acetate condition, genes related to flagellar assembly and membrane proteins were differentially expressed such as the general transcription factors fliA, flhD, flhC, and flagellum assembly genes were detected in E. coli, whereas in S. pombe genes for hexose transporters, integral membrane proteins, galactose metabolism, and ncRNAs related to cellular stress were overexpressed. In general, our study shows that a conserved "foraging behavior" response is observed in these eukaryotic and eubacterial organisms in gluconeogenic carbon sources.
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Affiliation(s)
- Joivier Vichi
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Verónica Jiménez Jacinto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Leticia Olvera Rodriguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ricardo Grande
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Dantán-González
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
- * E-mail:
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Krokidis MG, Exarchos TP, Vlamos P. Data-driven biomarker analysis using computational omics approaches to assess neurodegenerative disease progression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1813-1832. [PMID: 33757212 DOI: 10.3934/mbe.2021094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The complexity of biological systems suggests that current definitions of molecular dysfunctions are essential distinctions of a complex phenotype. This is well seen in neurodegenerative diseases (ND), such as Alzheimer's disease (AD) and Parkinson's disease (PD), multi-factorial pathologies characterized by high heterogeneity. These challenges make it necessary to understand the effectiveness of candidate biomarkers for early diagnosis, as well as to obtain a comprehensive mapping of how selective treatment alters the progression of the disorder. A large number of computational methods have been developed to explain network-based approaches by integrating individual components for modeling a complex system. In this review, high-throughput omics methodologies are presented for the identification of potent biomarkers associated with AD and PD pathogenesis as well as for monitoring the response of dysfunctional molecular pathways incorporating multilevel clinical information. In addition, principles for efficient data analysis pipelines are being discussed that can help address current limitations during the experimental process by increasing the reproducibility of benchmarking studies.
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Affiliation(s)
- Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Themis P Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Genomics-based approaches to identify and predict the health-promoting and safety activities of promising probiotic strains – A probiogenomics review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.12.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lin M, Sun S, Fang J, Qi X, Sun L, Zhong Y, Sun Y, Hong G, Wang R, Li Y. BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. BMC Genomics 2021; 22:72. [PMID: 33482717 PMCID: PMC7821520 DOI: 10.1186/s12864-021-07369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/05/2021] [Indexed: 01/02/2023] Open
Abstract
Background Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia arguta has excellent cold resistance, but knowledge relevant to molecular mechanisms is still limited. Understanding the mechanism underlying cold resistance in kiwifruit is important for breeding cold resistance. Results In our study, a population resulting from the cross of A. arguta ‘Ruby-3’ × ‘Kuilv’ male was generated for kiwifruit hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to their LT50. Then, we performed bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes that provide cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold-tolerant population than in the cold-sensitive population. Upon − 30 °C low-temperature treatment, 126 differentially expressed genes were identify; the expression of 59 genes was up-regulated and that of 67 genes was down-regulated between the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs were primarily related to starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Ten major key enzyme-encoding genes and two regulatory genes were up-regulated in the tolerant pool, and regulatory genes of the CBF pathway were found to be differentially expressed. In particular, a 14–3-3 gene was down-regulated and an EBF gene was up-regulated. To validate the BSR-Seq results, 24 DEGs were assessed via qRT-PCR, and the results were consistent with those obtained by BSR-Seq. Conclusion Our research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07369-9.
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Affiliation(s)
- Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shihang Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China.
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yanxiang Sun
- Langfang Normal University, Langfang, 065000, China
| | - Gu Hong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Ran Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Yukuo Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450000, China
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Whole blood transcriptome analysis using RNA sequencing in individuals with insomnia disorder and good sleepers: a pilot study. Sleep Med 2021; 80:1-8. [PMID: 33530007 DOI: 10.1016/j.sleep.2021.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Insomnia is a highly prevalent condition that is associated with negative health outcomes, yet little is known about the underlying molecular mechanisms. METHOD RNA sequencing was conducted using blood samples from 15 individuals with primary insomnia and 15 age- and gender-matched good sleeper controls. The RNA library was sequenced with 150 base pair paired-ends on the Illumina NovaSeq-6000 platform. Alignment was performed using human reference genome hg38. Differential gene expression analysis was performed using DESeq2 following alignment, using log fold change ±0.50, and had a false discovery rate p-value <0.05. Pathway analysis was performed using Ingenuity Pathway Analysis. RESULTS We found 288 differentially expressed genes in insomnia patients when compared to controls. Upregulated genes included LINC02224 (Long Intergenic Non-Protein Coding RNA 2224), DUX4L9 (Double Homeobox 4 Like 9), and TUSC3 (Tumor Suppressor Candidate 3) and down regulated genes included CTXN2 (Cortexin 2), CSMD1 (CUB And Sushi Multiple Domains 1), and SLC12A1 (Solute Carrier Family 12 Member 1). Ingenuity® Pathway Analysis (IPA) revealed 3 associated networks (score>40) with genes and hubs related to inflammation (nuclear factor-kB), oxidative stress (Mitochondrial complex 1) and ubiquitination. CONCLUSION Differentially expressed genes in this analysis are functionally associated with inflammation and immune response, mitochondrial and metabolic processes. Further research into the transcriptomic changes in insomnia is needed to understand related pathways to the disorder and provide new avenues for diagnostics and therapeutics.
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