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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Yang Y, Wen X, Wu Z, Wang K, Zhu Y. Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1711-1724. [PMID: 37079218 DOI: 10.1007/s11427-022-2341-8] [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: 12/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii genome is occupied by TEs. In this study, we investigated whether there were unknown transcripts associated with TE or TE fragments and, if so, how these new transcripts were evolved and regulated. As sequence depths increased from 4 to 100 G, a total of 10,284 novel intergenic transcripts (intergenic genes) were discovered. On average, approximately 84% of these intergenic transcripts possibly overlapped with the long terminal repeat (LTR) insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels. Most of these intergenic transcripts possessed no transcription activation markers, while the majority of the regular genic genes possessed at least one such marker. Genes without transcription activation markers formed their+1 and -1 nucleosomes more closely (only (117±1.4)bp apart), while twice as big spaces (approximately (403.5±46.0) bp apart) were detected for genes with the activation markers. The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content. Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7 million years ago (MYA) for all eudicot genomes or 13.7 MYA for the Gossypium family, respectively, while the intergenic transcripts evolved around 1.6 MYA, resultant of the last LTR insertion. The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.
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Affiliation(s)
- Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hubei Hongshan Laboratory, Wuhan, 430072, China.
- TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, 430072, China.
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Zheng J, Wen S, Yu Z, Luo K, Rong J, Ding M. Alternative Splicing during Fiber Development in G. hirsutum. Int J Mol Sci 2023; 24:11812. [PMID: 37511571 PMCID: PMC10380772 DOI: 10.3390/ijms241411812] [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: 05/29/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in Gossypium hirsutum. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon-intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.
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Affiliation(s)
- Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Keyan Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
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Wang S, Wu H, Zhao Y, Wang L, Guan X, Zhao T. Mapping intron retention events contributing to complex traits using splice quantitative trait locus. PLANT METHODS 2023; 19:72. [PMID: 37480119 PMCID: PMC10362629 DOI: 10.1186/s13007-023-01048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Alternative splicing (AS) of mRNA plays an important roles in transcriptome diversity, involving regulation of plant growth and stress response. Understanding the variation of AS events underlying GWAS loci in a crop population can provide insight into the molecular mechanisms of complex agronomic traits. To date, genome-wide association studies relating AS events to agronomic traits have rarely been conducted at the population level in crops. RESULTS Here, a pipeline was constructed to identify candidate AS events related to complex traits. Firstly, ovule transcriptome data were used to characterize intron retention (IR), the predominant type of AS in plants, on a genome-wide scale. This was done in a natural population consisting of 279 upland cotton lines. Secondly, splice quantitative trait locus (sQTL) analysis was carried out, which yielded a total of 2295 sQTLs involving 1607 genes. Of these, 14.25% (n = 427) were cis-regulatory loci. Integration with expression quantitative trait loci (eQTL) revealed that 53 (21.4%) cis-sGenes were regulated by both cis-sQTLs and cis-eQTLs. Finally, co-localization analysis integrated with GWAS loci in this population showed 32 cis-QTLs to be co-located with genetic regulatory loci related to fiber yield and quality traits, indicating that sQTLs are likely to participate in regulating cotton fiber yield and quality. An in-depth evaluation confirmed that differences in the IR rates of sQTL-regulated candidate genes such as GhLRRK1 and GhGC1 are associated with lint percentage (LP), which has potential in breeding applications. CONCLUSION This study provides a clue that AS of mRNA has an impact on crop yield, along with functional sQTLs are new genetic resources for cotton precision breeding.
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Affiliation(s)
- Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
| | - Yongyan Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
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Misra CS, Sousa AGG, Barros PM, Kermanov A, Becker JD. Cell-type-specific alternative splicing in the Arabidopsis germline. PLANT PHYSIOLOGY 2023; 192:85-101. [PMID: 36515615 PMCID: PMC10152659 DOI: 10.1093/plphys/kiac574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 05/03/2023]
Abstract
During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.
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Affiliation(s)
- Chandra Shekhar Misra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Anton Kermanov
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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Rasool A, Azeem F, Ur-Rahman M, Rizwan M, Hussnain Siddique M, Bay DH, Binothman N, Al Kashgry NAT, Qari SH. Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid. FRONTIERS IN PLANT SCIENCE 2023; 14:1138048. [PMID: 37063177 PMCID: PMC10102465 DOI: 10.3389/fpls.2023.1138048] [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: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The two-component system (TCS) genes are involved in a wide range of physiological processes in prokaryotes and eukaryotes. In plants, the TCS elements help in a variety of functions, including cell proliferation, response to abiotic and biotic stresses, leaf senescence, nutritional signaling, and division of chloroplasts. Three different kinds of proteins make up the TCS system in plants. These are known as HKs (histidine kinases), HPs (histidine phosphotransfer), and RRs (response regulators). We investigated the genome of Gossypium raimondii and discovered a total of 59 GrTCS candidates, which include 23 members of the HK family, 8 members of the HP family, and 28 members of the RR family. RR candidates are further classified as type-A (6 members), type-B (11 members), type-C (2 members), and pseudo-RRs (9 members). The GrTCS genes were analyzed in comparison with the TCS components of other plant species such as Arabidopsis thaliana, Cicer arietinum, Sorghum bicolor, Glycine max, and Oryza sativa. This analysis revealed both conservation and changes in their structures. We identified 5 pairs of GrTCS syntenic homologs in the G. raimondii genome. All 59 TCS genes in G. raimondii are located on all thirteen chromosomes. The GrTCS promoter regions have several cis-regulatory elements, which function as switches and respond to a wide variety of abiotic stresses. RNA-seq and real-time qPCR analysis showed that the majority of GrTCS genes are differentially regulated in response to salt and cold stress. 3D structures of GrTCS proteins were predicted to reveal the specific function. GrTCSs were docked with abscisic acid to assess their binding interactions. This research establishes the groundwork for future functional studies of TCS elements in G. raimondii, which will further focus on stress resistance and overall development.
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Affiliation(s)
- Asima Rasool
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahmood Ur-Rahman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hussnain Siddique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Daniyah Habiballah Bay
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | | | - Sameer H. Qari
- Department of Biology, A1-Jumum University College, Umm A1-Qura University, Makkah, Saudi Arabia
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Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads. Gene 2023; 852:147065. [PMID: 36435508 DOI: 10.1016/j.gene.2022.147065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are common mechanisms in eukaryotes to increase the complexity of transcriptomes and subsequently proteomes. Analysis of long reads transcriptomics data can result in the discovery of novel transcripts, splice sites, AS or APA events. Gossypium arboreum is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Specifically, its variety 'FDH228' is considered to be an important resistance source. In this study, we sequenced the G. arboreum (var. FDH228) transcriptome using PacBio IsoSeq and illumina short read sequencing under three different conditions i.e. untreated/healthy, treated with biotic stress through whitefly infestation, and treated with abiotic stress via water deprivation, for the discovery and surveying of canonical and non-canonical AS, APA and transcript fusion events. We were able to obtain 15,419 unique transcripts from all samples representing 11,343 genes, out of which 10,832 were annotated and 520 were novel with respect to the published reference genome. These transcripts were grouped into different structural categories including 60 Antisense, 11,959 having a full-splice match, 999 with incomplete-splice match, 30 fusion transcripts, 177 genic, 479 intergenic, 771 novels in the catalog, and 944 Novel but not found in the catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, and novel and fusion transcripts aids in the understanding of the resistance mechanisms for this specific germplasm.
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The Function of DNA Demethylase Gene ROS1a Null Mutant on Seed Development in Rice ( Oryza Sativa) Using the CRISPR/CAS9 System. Int J Mol Sci 2022; 23:ijms23126357. [PMID: 35742811 PMCID: PMC9223687 DOI: 10.3390/ijms23126357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 02/05/2023] Open
Abstract
The endosperm is the main nutrient source in cereals for humans, as it is a highly specialized storage organ for starch, lipids, and proteins, and plays an essential role in seed growth and development. Active DNA demethylation regulates plant developmental processes and is ensured by cytosine methylation (5-meC) DNA glycosylase enzymes. To find out the role of OsROS1a in seed development, the null mutant of OsROS1a was generated using the CRISPR/Cas9 system. The null mutant of OsROS1a was stable and heritable, which affects the major agronomic traits, particularly in rice seeds. The null mutant of OsROS1a showed longer and narrower grains, and seeds were deformed containing an underdeveloped and less-starch-producing endosperm with slightly irregularly shaped embryos. In contrast to the transparent grains of the wild type, the grains of the null mutant of OsROS1a were slightly opaque and rounded starch granules, with uneven shapes, sizes, and surfaces. A total of 723 differential expression genes (DEGs) were detected in the null mutant of OsROS1a by RNA-Seq, of which 290 were downregulated and 433 were upregulated. The gene ontology (GO) terms with the top 20 enrichment factors were visualized for cellular components, biological processes, and molecular functions. The key genes that are enriched for these GO terms include starch synthesis genes (OsSSIIa and OsSSIIIa) and cellulose synthesis genes (CESA2, CESA3, CESA6, and CESA8). Genes encoding polysaccharides and glutelin were found to be downregulated in the mutant endosperm. The glutelins were further verified by SDS-PAGE, suggesting that glutelin genes could be involved in the null mutant of OsROS1a seed phenotype and OsROS1a could have the key role in the regulation of glutelins. Furthermore, 378 differentially alternative splicing (AS) genes were identified in the null mutant of OsROS1a, suggesting that the OsROS1a gene has an impact on AS events. Our findings indicated that the function on rice endosperm development in the null mutant of OsROS1a could be influenced through regulating gene expression and AS, which could provide the base to properly understand the molecular mechanism related to the OsROS1a gene in the regulation of rice seed development.
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Satheesh V, Zhang J, Li J, You Q, Zhao P, Wang P, Lei M. High transcriptome plasticity drives phosphate starvation responses in tomato. STRESS BIOLOGY 2022; 2:18. [PMID: 37676521 PMCID: PMC10441952 DOI: 10.1007/s44154-022-00035-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/11/2022] [Indexed: 09/08/2023]
Abstract
Tomato is an important vegetable crop and fluctuating available soil phosphate (Pi) level elicits several morpho-physiological responses driven by underlying molecular responses. Therefore, understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency. A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato. Apart from changes in the expression levels of genes, there were also alterations in the expression of alternatively-spliced transcripts. Physiological responses such as anthocyanin accumulation, reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses (PSR). Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato. Overall, our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare. Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.
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Affiliation(s)
- Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jieqiong Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jinkai Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qiuye You
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Panfeng Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Peng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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Azeem F, Zameer R, Rehman Rashid MA, Rasul I, Ul-Allah S, Siddique MH, Fiaz S, Raza A, Younas A, Rasool A, Ali MA, Anwar S, Siddiqui MH. Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:110-122. [PMID: 34864561 DOI: 10.1016/j.plaphy.2021.11.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.
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Affiliation(s)
- Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | | | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahauddin Zakariya University, Bahadur Sub-Campus, Layyah, Pakistan
| | | | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, 22620, Haripir, Pakistan.
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, 350002, China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Asima Rasool
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Sultana Anwar
- Department of Agronomy, University of Florida, Gainesville, USA
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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11
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Zhang M, Li N, Yang W, Liu B. Genome-wide differences in gene expression and alternative splicing in developing embryo and endosperm, and between F1 hybrids and their parental pure lines in sorghum. PLANT MOLECULAR BIOLOGY 2022; 108:1-14. [PMID: 34846608 DOI: 10.1007/s11103-021-01196-y] [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: 06/03/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Developing embryo and endosperm of sorghum show substantial and multifaceted differences in gene expression and alternative splicing, which are potentially relevant to heterosis. Differential regulation of gene expression and alternative splicing (AS) are major molecular mechanisms dictating plant growth and development, as well as underpinning heterosis in F1 hybrids. Here, using deep RNA-sequencing we analyzed differences in genome-wide gene expression and AS between developing embryo and endosperm, and between F1 hybrids and their pure-line parents in sorghum. We uncover dramatic differences in both gene expression and AS between embryo and endosperm with respect to gene features and functions, which are consistent with the fundamentally different biological roles of the two tissues. Accordingly, F1 hybrids showed substantial and multifaceted differences in gene expression and AS compared with their pure-line parents, again with clear tissue specificities including extents of difference, genes involved and functional enrichments. Our results provide useful transcriptome resources as well as novel insights for further elucidation of seed yield heterosis in sorghum and related crops.
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Affiliation(s)
- Meishan Zhang
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Weiguang Yang
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People's Republic of China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
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12
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Heyduk K, McAssey EV, Grimwood J, Shu S, Schmutz J, McKain MR, Leebens-Mack J. Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae). FRONTIERS IN PLANT SCIENCE 2021; 11:573767. [PMID: 33519836 PMCID: PMC7843428 DOI: 10.3389/fpls.2020.573767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/17/2020] [Indexed: 05/23/2023]
Abstract
Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ∼11 kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from 41 accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case-Copia LTR transposons-did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.
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Affiliation(s)
- Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Edward V. McAssey
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Biological Sciences, Quinnipiac University, Hamden, CT, United States
- Department of Biology and Environmental Science, University of New Haven, West Haven, CT, United States
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shengqiang Shu
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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13
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Lin A, Ma J, Xu F, Xu W, Jiang H, Zhang H, Qu C, Wei L, Li J. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. PLANTS (BASEL, SWITZERLAND) 2020; 9:E977. [PMID: 32752101 PMCID: PMC7465011 DOI: 10.3390/plants9080977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022]
Abstract
Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.
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Affiliation(s)
- Ai Lin
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jinqi Ma
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Fei Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Wen Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Huanhuan Jiang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Lijuan Wei
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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14
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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15
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Tanaka Y, Asano T, Kanemitsu Y, Goto T, Yoshida Y, Yasuba K, Misawa Y, Nakatani S, Kobata K. Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:693-705. [PMID: 31323150 DOI: 10.1111/tpj.14462] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Capsaicinoids are unique compounds that give chili pepper fruits their pungent taste. Capsaicinoid levels vary widely among pungent cultivars, which range from low pungency to extremely pungent. However, the molecular mechanisms underlying this quantitative variation have not been elucidated. Our previous study identified various loss-of-function alleles of the pAMT gene which led to low pungency. The mutations in these alleles are commonly defined by Tcc transposon insertion and its footprint. In this study, we identified two leaky pamt alleles (pamtL1 and pamtL2 ) with different levels of putative aminotransferase (pAMT) activity. Notably, both alleles had a Tcc transposon insertion in intron 3, but the locations of the insertions within the intron were different. Genetic analysis revealed that pamtL1 , pamtL2 and a loss-of-function pamt allele reduced capsaicinoid levels to about 50%, 10% and less than 1%, respectively. pamtL1 and pamtL2 encoded functional pAMT proteins, but they exhibited lower transcript levels than the functional type. RNA sequencing analysis showed that intronic transposons disrupted splicing in intron 3, which resulted in simultaneous expression of functional pAMT mRNA and non-functional splice variants containing partial sequences of Tcc. The non-functional splice variants were more dominant in pamtL2 than in pamtL1 . This suggested that the difference in position of the intronic transposons could alter splicing efficiency, leading to different pAMT activities and reducing capsaicinoid content to different levels. Our results provide a striking example of allelic variations caused by intronic transposons; these variations contribute to quantitative differences in secondary metabolite contents.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takaya Asano
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yorika Kanemitsu
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Misawa
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Sachie Nakatani
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Kenji Kobata
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
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16
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Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nat Commun 2019; 10:4714. [PMID: 31624240 PMCID: PMC6797763 DOI: 10.1038/s41467-019-12575-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022] Open
Abstract
Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
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17
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Yang Y, Pu Y, Yin X, Du J, Zhou Z, Yang D, Sun X, Sun H, Yang Y. A Splice Variant of BrrWSD1 in Turnip ( Brassica rapa var. rapa) and Its Possible Role in Wax Ester Synthesis under Drought Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11077-11088. [PMID: 31525039 DOI: 10.1021/acs.jafc.9b04069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cuticular wax accumulation in plants contributes to drought tolerance. Here, we compared the drought levels on two varieties with different genotypes in turnip (Brassica rapa var. rapa) and found that the drought tolerance was higher in the waxy KTRG-B48a than in the wax-free KTRG-B48b. A combination of PacBio and Illumina sequencing analyses revealed that differential transcripts were mainly enriched in the wax synthesis pathway, and a splice variant (BrrWSD1-X2) was identified in the waxy KTRG-B48a. BrrWSD1-X2 had a stronger ability to synthesize wax esters than BrrWSD1-X1 using heterologous expression in yeast (Saccharomyces cerevisiae) mutant H1246a. Then, we speculated that the T to C transversion of the third intron and the higher number of TA repeats in the third intron of BrrWSD1 DNA in the waxy KTRG-B48a may result in a lower efficiency of splicing recognition of the third intron, resulting in the emergence of BrrWSD1-X2 in waxy varieties.
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Affiliation(s)
- Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
| | - Yanan Pu
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
| | - Xin Yin
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jiancan Du
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
| | - Zhili Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
| | - Danni Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Xudong Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia , Kunming Institute of Botany, Chinese Academy of Science , Kunming , 650204 , People's Republic of China
- Plant Germplasm and Genomics Center , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- Institute of Tibetan Plateau Research at Kunming , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , 650201 , People's Republic of China
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18
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Zhang Z, Fu T, Liu Z, Wang X, Xun H, Li G, Ding B, Dong Y, Lin X, Sanguinet KA, Liu B, Wu Y, Gong L. Extensive changes in gene expression and alternative splicing due to homoeologous exchange in rice segmental allopolyploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2295-2308. [PMID: 31098756 DOI: 10.1007/s00122-019-03355-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
We report rampant homoeologous exchanges in progenies of a newly synthesized rice segmental allotetraploid and demonstrate their consequences to changes of gene expression and alternative splicing. Allopolyploidization is recurrent across the tree of angiosperms and known as a driving evolutionary force in both plants and animals. A salient feature of allopolyploidization is the induction of homoeologous exchange (HE) events between the constituent subgenomes, which may in turn cause changes in gene expression, transcript alternative splicing, and phenotypic novelty. However, this issue has been poorly studied, largely because lack of a system in which the exact parentage donating the subgenomes is known and the HE events are occurring in real time. Here, we employed whole-genome re-sequencing and RNA-seq-based transcriptome profiling in four randomly chosen progeny individuals (at the 10th-selfed generation) of segmental allotetraploids that were constructed by colchicine-mediated whole-genome doubling of F1 hybrids between the two subspecies (japonica and indica) of Asian cultivated Oryza sativa. We show that rampant HE events occurred in these tetraploid individuals, which converted most of the otherwise heterozygous genomic regions into a homogenized state of one parental subgenome. We demonstrate that genes within these homogenized genomic regions in the tetraploids showed high frequencies of altered expression and enhanced alternative splicing relative to their counterparts in the corresponding diploid parents in the embryo tissue. Intriguingly, limited overlaps between the differentially expressed genes and the differential alternative spliced genes were identified, which were partitioned to distinctly enriched gene ontology terms. Together, our results indicate that HE is a major mechanism to rapidly generate novelty in gene expression and transcriptome diversity, which may facilitate phenotypic innovation in nascent allopolyploids and relevant to allopolyploid crop breeding.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tiansi Fu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhijian Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Baoxu Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences (JAAS), Changchun, 136100, China
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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Sharif I, Aleem S, Farooq J, Rizwan M, Younas A, Sarwar G, Chohan SM. Salinity stress in cotton: effects, mechanism of tolerance and its management strategies. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:807-820. [PMID: 31402811 PMCID: PMC6656830 DOI: 10.1007/s12298-019-00676-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/15/2019] [Accepted: 05/13/2019] [Indexed: 05/21/2023]
Abstract
Cotton is classified as moderately salt tolerant crop with salinity threshold level of 7.7 dS m-1. Salinity is a serious threat for cotton growth, yield and fiber quality. The sensitivity to salt stress depends upon growth stage and type of salt. Understanding of cotton response to salinity, its resistance mechanism and looking into management techniques may assist in formulating strategies to improve cotton performance under saline condition. The studies have showed that germination, emergence and seedling stages are more sensitive to salinity stress as compared to later stages. Salt stress results in delayed flowering, less fruiting positions, fruit shedding and reduced boll weight which ultimately affect seed cotton yield. Depressed activities of metabolic enzymes viz: acidic invertase, alkaline invertase and sucrose phophate synthase lead to fiber quality deterioration in salinity. Excessive sodium exclusion or its compartmentation is the main adaptive mechanism in cotton under salt stress. Up regulation of enzymatic and non-enzymatic antioxidants genes offer important adaptive potential to develop salt tolerant cotton varieties. Seed priming is also an effective approach for improving cotton germination in saline soils. Intra and inter variation in cotton germplasm could be used to develop salt tolerant varieties with the aid of marker assisted selection. Furthermore, transgenic approach could be the promising option for enhancing cotton production under saline condition. It is suggested that future research may be carried out with the combination of conventional and advance molecular technology to develop salt tolerant cultivars.
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Affiliation(s)
- Iram Sharif
- Cotton Research Station, AARI, Faisalabad, Pakistan
| | - Saba Aleem
- Vegetable Research Institute, AARI, Faisalabad, Pakistan
| | | | | | - Abia Younas
- Cotton Research Station, AARI, Faisalabad, Pakistan
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Ma B, Xin Y, Kuang L, He N. Distribution and Characteristics of Transposable Elements in the Mulberry Genome. THE PLANT GENOME 2019; 12:180094. [PMID: 31290922 DOI: 10.3835/plantgenome2018.12.0094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mulberry ( C. K. Schneid) leaves have been used as the food for the domesticated silkworm, , for more than 5000 yr, and the mulberry-silkworm relationship is one of the best-known and oldest models of plant defense-insect adaptation. The availability of a genome assembly of mulberry provides us with an opportunity to mine the characteristics and distribution of transposable elements (TEs) in this species and to examine their relationship to genes and gene expression. In this study, a significantly correlated inverse relationship between the percentage coverage of genes and TEs was observed. The TE-rich regions appeared to have a lower percentage of putatively expressed genes. Distribution patterns between different TE superfamilies were detected in the mulberry genome. The elements (the TE making up the greatest proportion of the mulberry genome) were significantly overrepresented within genes in the mulberry genome, and they may have a dominant influence on evolution of the mulberry genome. Approximately 96.93% (330/344) of the TE-containing genes assigned to pathways were assigned to metabolism-related pathways. The TE-related alternative splicing events accounted for 7.58% (402/5,302) of all alternative splicing types in the mulberry genome, suggesting that TEs are one of the driving forces in the formation of the alternatively spliced genes. The results will be valuable in improving our understanding of the important roles of TEs in mulberry genome evolution.
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Brassica napus Infected with Leptosphaeria maculans. Genes (Basel) 2019; 10:genes10040296. [PMID: 30979089 PMCID: PMC6523698 DOI: 10.3390/genes10040296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 01/07/2023] Open
Abstract
Alternative splicing (AS) is a post-transcriptional regulatory process that enhances transcriptome diversity, thereby affecting plant growth, development, and stress responses. To identify the new transcripts and changes in the isoform-level AS landscape of rapeseed (Brassica napus) infected with the fungal pathogen Leptosphaeria maculans, we compared eight RNA-seq libraries prepared from mock-inoculated and inoculated B. napus cotyledons and stems. The AS events that occurred in stems were almost the same as those in cotyledons, with intron retention representing the most common AS pattern. We identified 1892 differentially spliced genes between inoculated and uninoculated plants. We performed a weighted gene co-expression network analysis (WGCNA) to identify eight co-expression modules and their Hub genes, which are the genes most connected with other genes within each module. There are nine Hub genes, encoding nine transcription factors, which represent key regulators of each module, including members of the NAC, WRKY, TRAF, AP2/ERF-ERF, C2H2, C2C2-GATA, HMG, bHLH, and C2C2-CO-like families. Finally, 52 and 117 alternatively spliced genes in cotyledons and stems were also differentially expressed between mock-infected and infected materials, such as HMG and C2C2-Dof; which have dual regulatory mechanisms in response to L. maculans. The splicing of the candidate genes identified in this study could be exploited to improve resistance to L. maculans.
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Song QA, Catlin NS, Brad Barbazuk W, Li S. Computational analysis of alternative splicing in plant genomes. Gene 2019; 685:186-195. [PMID: 30321657 DOI: 10.1016/j.gene.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 09/16/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
Abstract
Computational analyses play crucial roles in characterizing splicing isoforms in plant genomes. In this review, we provide a survey of computational tools used in recently published, genome-scale splicing analyses in plants. We summarize the commonly used software and pipelines for read mapping, isoform reconstruction, isoform quantification, and differential expression analysis. We also discuss methods for analyzing long reads and the strategies to combine long and short reads in identifying splicing isoforms. We review several tools for characterizing local splicing events, splicing graphs, coding potential, and visualizing splicing isoforms. We further discuss the procedures for identifying conserved splicing isoforms across plant species. Finally, we discuss the outlook of integrating other genomic data with splicing analyses to identify regulatory mechanisms of AS on genome-wide scale.
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Affiliation(s)
- Qi A Song
- Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Nathan S Catlin
- Department of Biology, University of Florida, Gainesville, FL 32611, United States of America
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL 32611, United States of America; Genetics Institute, University of Florida, Gainesville, FL 32611, United States of America
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America.
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Yu X, Meng X, Liu Y, Wang X, Wang TJ, Zhang A, Li N, Qi X, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress. PLANT CELL REPORTS 2019; 38:131-145. [PMID: 30443733 DOI: 10.1007/s00299-018-2354-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/07/2018] [Indexed: 05/16/2023]
Abstract
Maize SWI3-type chromatin remodeler impacts alternative splicing contexts in response to osmotic stress by altering nucleosome density and affecting transcriptional elongation rate. Alternative splicing (AS) is commonly found in higher eukaryotes and is an important posttranscriptional regulatory mechanism to generate transcript diversity. AS has been widely accepted as playing essential roles in different biological processes including growth, development, signal transduction and responses to biotic and abiotic stresses in plants. However, whether and how chromatin remodeling complex functions in AS in plant under osmotic stress remains unknown. Here, we show that a maize SWI3D protein, ZmCHB101, impacts AS contexts in response to osmotic stress. Genome-wide analysis of mRNA contexts in response to osmotic stress using ZmCHB101-RNAi lines reveals that ZmCHB101 impacts alternative splicing contexts of a subset of osmotic stress-responsive genes. Intriguingly, ZmCHB101-mediated regulation of gene expression and AS is largely uncoupled, pointing to diverse molecular functions of ZmCHB101 in transcriptional and posttranscriptional regulation. We further found ZmCHB101 impacts the alternative splicing contexts by influencing alteration of chromatin and histone modification status as well as transcriptional elongation rates mediated by RNA polymerase II. Taken together, our findings suggest a novel insight of how plant chromatin remodeling complex impacts AS under osmotic stress .
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Affiliation(s)
- Xiaoming Yu
- School of Agronomy, Jilin Agricultural Science and Technology University, Jilin, 132301, People's Republic of China
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
- Department of Agronomy, Purdue University, West Lafayette, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
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Clark S, Yu F, Gu L, Min XJ. Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato. FRONTIERS IN PLANT SCIENCE 2019; 10:689. [PMID: 31191588 PMCID: PMC6546887 DOI: 10.3389/fpls.2019.00689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/08/2019] [Indexed: 05/17/2023]
Abstract
Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).
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Affiliation(s)
- Sarah Clark
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
| | - Feng Yu
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Jia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
- *Correspondence: Xiang Jia Min,
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Zhao H, Gao Z, Wang L, Wang J, Wang S, Fei B, Chen C, Shi C, Liu X, Zhang H, Lou Y, Chen L, Sun H, Zhou X, Wang S, Zhang C, Xu H, Li L, Yang Y, Wei Y, Yang W, Gao Q, Yang H, Zhao S, Jiang Z. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). Gigascience 2018; 7:5092772. [PMID: 30202850 PMCID: PMC6204424 DOI: 10.1093/gigascience/giy115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Background Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Le Wang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.,Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA
| | - Jiongliang Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Songbo Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, No. 7 PengFei Rd, Dapeng District, Shenzhen 518120, China
| | - Benhua Fei
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Chengcheng Shi
- BGI-Qingdao, No. 2877, Tuanjie Rd, Sino-German Ecopark, Qingdao, Shandong Province, 266555, China
| | - Xiaochuan Liu
- BGI-Qingdao, No. 2877, Tuanjie Rd, Sino-German Ecopark, Qingdao, Shandong Province, 266555, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Yongfeng Lou
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - LianFu Chen
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Huayu Sun
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Xianqiang Zhou
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Sining Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Hao Xu
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Lichao Li
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Yihong Yang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
| | - Yanli Wei
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Wei Yang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Huanming Yang
- BGI Genomics, BGI-Shenzhen, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, No. 7 PengFei Rd, Dapeng District, Shenzhen 518120, China
| | - Zehui Jiang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Futongdong Rd, WangJing, Chaoyang District Beijing 100102, China
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Ruan J, Guo F, Wang Y, Li X, Wan S, Shan L, Peng Z. Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.). BMC PLANT BIOLOGY 2018; 18:139. [PMID: 29973157 PMCID: PMC6032549 DOI: 10.1186/s12870-018-1339-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 06/04/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Alternative splicing (AS) represents a mechanism widely used by eukaryotes for the post-transcriptional regulation of genes. The detailed exploration of AS in peanut has not been documented. RESULTS The strand-specific RNA-Seq technique was exploited to characterize the distribution of AS in the four samples of peanut (FH1-seed1, FH1-seed2, FH1-root and FH1-leaf). AS was detected as affecting around 37.2% of the full set of multi-exon genes. Some of these genes experienced AS throughout the plant, while in the case of others, the effect was organ-specific. Overall, AS was more frequent in the seed than in either the root or leaf. The predominant form of AS was intron retention, and AS in transcription start site and transcription terminal site were commonly identified in all the four samples. It is interesting that in genes affected by AS, the majority experienced only a single type of event. Not all of the in silico predicted transcripts appeared to be translated, implying that these are either degraded or sequestered away from the translation machinery. With respect to genes involved in fatty acid metabolism, about 61.6% were shown to experience AS. CONCLUSION Our report contributes significantly in AS analysis of peanut genes in general, and these results have not been mentioned before. The specific functions of different AS forms need further investigation.
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Affiliation(s)
- Jian Ruan
- College of Life Science, Shandong University, Jinan, China
| | - Feng Guo
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Yingying Wang
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Xinguo Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Shubo Wan
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Lei Shan
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
| | - Zhenying Peng
- College of Life Science, Shandong University, Jinan, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, China
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Wang W, Zhou Y, Wu Y, Dai X, Liu Y, Qian Y, Li M, Jiang X, Wang Y, Gao L, Xia T. Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:4281-4293. [PMID: 29606002 DOI: 10.1021/acs.jafc.8b00946] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tea is an important economic crop with a 3.02 Gb genome. It accumulates various bioactive compounds, especially catechins, which are closely associated with tea flavor and quality. Catechins are biosynthesized through the phenylpropanoid and flavonoid pathways, with 12 structural genes being involved in their synthesis. However, we found that in Camellia sinensis the understanding of the basic profile of catechins biosynthesis is still unclear. The gene structure, locus, transcript number, transcriptional variation, and function of multigene families have not yet been clarified. Our previous studies demonstrated that the accumulation of flavonoids in tea is species, tissue, and induction specific, which indicates that gene coexpression patterns may be involved in tea catechins and flavonoids biosynthesis. In this paper, we screened candidate genes of multigene families involved in the phenylpropanoid and flavonoid pathways based on an analysis of genome and transcriptome sequence data. The authenticity of candidate genes was verified by PCR cloning, and their function was validated by reverse genetic methods. In the present study, 36 genes from 12 gene families were identified and were accessed in the NCBI database. During this process, some intron retention events of the CsCHI and CsDFR genes were found. Furthermore, the transcriptome sequencing of various tea tissues and subcellular location assays revealed coexpression and colocalization patterns. The correlation analysis showed that CsCHIc, CsF3'H, and CsANRb expression levels are associated significantly with the concentration of soluble PA as well as the expression levels of CsPALc and CsPALf with the concentration of insoluble PA. This work provides insights into catechins metabolism in tea and provides a foundation for future studies.
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Affiliation(s)
- Wenzhao Wang
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Yihui Zhou
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Yingling Wu
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Xinlong Dai
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Yajun Liu
- School of Life Science , Anhui Agricultural University , Hefei 230036 , China
| | - Yumei Qian
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
- School of Biological and Food Engineering , Suzhou University , 49 Middle Bianhe Road , Suzhou , 234000 Anhui , China
| | - Mingzhuo Li
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
- Department of Plant and Microbial Biology , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Xiaolan Jiang
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
| | - Yunsheng Wang
- School of Life Science , Anhui Agricultural University , Hefei 230036 , China
| | - Liping Gao
- School of Life Science , Anhui Agricultural University , Hefei 230036 , China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biochemistry and Utilization , Anhui Agricultural University , Hefei 230036 , China
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He P, Xiao G, Liu H, Zhang L, Zhao L, Tang M, Huang S, An Y, Yu J. Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. THE NEW PHYTOLOGIST 2018; 218:167-182. [PMID: 29417579 DOI: 10.1111/nph.14999] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/14/2017] [Indexed: 06/08/2023]
Abstract
RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length. Our results indicate that editing at C1292 and C1415 sites in Ghatp1 is crucial for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. This work extends our understanding of RNA editing in atp1 and ATP synthesis, and provides insights into the function of mitochondrial edited Atp1 protein in higher plants.
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Affiliation(s)
- Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hao Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Lihua Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Li Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Sheng Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yingjie An
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
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Liu Z, Qin J, Tian X, Xu S, Wang Y, Li H, Wang X, Peng H, Yao Y, Hu Z, Ni Z, Xin M, Sun Q. Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2018; 16:714-726. [PMID: 28834352 PMCID: PMC5814593 DOI: 10.1111/pbi.12822] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/17/2017] [Accepted: 08/10/2017] [Indexed: 05/13/2023]
Abstract
Plant can acquire tolerance to environmental stresses via transcriptome reprogramming at transcriptional and alternative splicing (AS) levels. However, how AS coordinates with transcriptional regulation to contribute to abiotic stresses responses is still ambiguous. In this study, we performed genome-wide analyses of AS responses to drought stress (DS), heat stress (HS) and their combination (HD) in wheat seedlings, and further compared them with transcriptional responses. In total, we found 200, 3576 and 4056 genes exhibiting significant AS pattern changes in response to DS, HS and HD, respectively, and combined drought and heat stress can induce specific AS compared with individual one. In addition, wheat homeologous genes exhibited differential AS responses under stress conditions that more AS events occurred on B subgenome than on A and D genomes. Comparison of genes regulated at AS and transcriptional levels showed that only 12% of DS-induced AS genes were subjected to transcriptional regulation, whereas the proportion increased to ~40% under HS and HD. Functional enrichment analysis revealed that abiotic stress-responsive pathways tended to be highly overrepresented among these overlapped genes under HS and HD. Thus, we proposed that transcriptional regulation may play a major role in response to DS, which coordinates with AS regulation to contribute to HS and HD tolerance in wheat.
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Affiliation(s)
- Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Jinxia Qin
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xuejun Tian
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Yu Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Hongxia Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Huiru Peng
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Yingyin Yao
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhaorong Hu
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Zhongfu Ni
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Mingming Xin
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
| | - Qixin Sun
- State Key Laboratory for AgrobiotechnologyKey Laboratory of Crop Heterosis Utilization (MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
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Zhu G, Li W, Zhang F, Guo W. RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii. BMC Genomics 2018; 19:73. [PMID: 29361913 PMCID: PMC5782385 DOI: 10.1186/s12864-018-4449-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/14/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Numerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the post-transcriptional level. RESULTS Using a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as "responses to stress", "metabolic process" and "RNA splicing", implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K+ channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stress. CONCLUSION This study first provide a comprehensive view of AS in G. davidsonii, and highlight novel insights into the potential roles of AS in plant responses to salt stress.
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Affiliation(s)
- Guozhong Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weixi Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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An D, Cao HX, Li C, Humbeck K, Wang W. Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. Genes (Basel) 2018; 9:genes9010043. [PMID: 29346292 PMCID: PMC5793194 DOI: 10.3390/genes9010043] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/30/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications. Such applications of Iso-Seq facilitate the understanding of gene structure, post-transcriptional regulatory networks, and subsequently proteomic diversity. In this review, we summarize its applications in plant transcriptome study, specifically pointing out challenges associated with each step in the experimental design and highlight the development of bioinformatic pipelines. We aim to provide the community with an integrative overview and a comprehensive guidance to Iso-Seq, and thus to promote its applications in plant research.
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Affiliation(s)
- Dong An
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
| | - Hieu X Cao
- Institute of Biology/Plant Physiology, Martin-Luther-University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany.
| | - Changsheng Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
| | - Klaus Humbeck
- Institute of Biology/Plant Physiology, Martin-Luther-University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany.
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
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Wang M, Wang P, Liang F, Ye Z, Li J, Shen C, Pei L, Wang F, Hu J, Tu L, Lindsey K, He D, Zhang X. A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. THE NEW PHYTOLOGIST 2018; 217:163-178. [PMID: 28892169 DOI: 10.1111/nph.14762] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/25/2017] [Indexed: 05/21/2023]
Abstract
Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (https://github.com/Nextomics/pipeline-for-isoseq). We identified 176 849 full-length transcript isoforms from 44 968 gene models and updated gene annotation. These data led us to identify 15 102 fibre-specific AS events and estimate that c. 51.4% of homoeologous genes produce divergent isoforms in each subgenome. We reveal that AS allows differential regulation of the same gene by miRNAs at the isoform level. We also show that nucleosome occupancy and DNA methylation play a role in defining exons at the chromatin level. This study provides new insights into the complexity and regulation of AS, and will enhance our understanding of AS in polyploid species. Our methodology for Iso-Seq data analysis will be a useful reference for the study of AS in other species.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Fan Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Feng Wang
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Jiang Hu
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Daohua He
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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Wu Z, Yang Y, Huang G, Lin J, Xia Y, Zhu Y. Cotton functional genomics reveals global insight into genome evolution and fiber development. J Genet Genomics 2017; 44:511-518. [PMID: 29169921 DOI: 10.1016/j.jgg.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/22/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.
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Affiliation(s)
- Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Lin
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuying Xia
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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Mao R, Liang C, Zhang Y, Hao X, Li J. 50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1728. [PMID: 29062321 PMCID: PMC5640774 DOI: 10.3389/fpls.2017.01728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/21/2017] [Indexed: 05/23/2023]
Abstract
Intron retention, one of the most prevalent alternative splicing events in plants, can lead to introns retained in mature mRNAs. However, in comparison with constitutively spliced introns (CSIs), the relevantly distinguishable features for retained introns (RIs) are still poorly understood. This work proposes a computational pipeline to discover novel RIs from multiple next-generation RNA sequencing (RNA-Seq) datasets of Arabidopsis thaliana. Using this pipeline, we detected 3,472 novel RIs from 18 RNA-Seq datasets and re-confirmed 1,384 RIs which are currently annotated in the TAIR10 database. We also use the expression of intron-containing isoforms as a new feature in addition to the conventional features. Based on these features, RIs are highly distinguishable from CSIs by machine learning methods, especially when the expressional odds of retention (i.e., the expression ratio of the RI-containing isoforms relative to the isoforms without RIs for the same gene) reaches to or larger than 50/50. In this case, the RIs and CSIs can be clearly separated by the Random Forest with an outstanding performance of 0.95 on AUC (the area under a receiver operating characteristics curve). The closely related characteristics to the RIs include the low strength of splice sites, high similarity with the flanking exon sequences, low occurrence percentage of YTRAY near the acceptor site, existence of putative intronic splicing silencers (ISSs, i.e., AG/GA-rich motifs) and intronic splicing enhancers (ISEs, i.e., TTTT-containing motifs), and enrichment of Serine/Arginine-Rich (SR) proteins and heterogeneous nuclear ribonucleoparticle proteins (hnRNPs).
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Affiliation(s)
- Rui Mao
- College of Information Engineering, Northwest A&F University, Yangling, China
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, United States
- Department of Computer Sciences and Software Engineering, Miami University, Oxford, OH, United States
| | - Yang Zhang
- College of Information Engineering, Northwest A&F University, Yangling, China
| | - Xingan Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jinyan Li
- Advanced Analytics Institute, University of Technology Sydney, Sydney, NSW, Australia
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Wei H, Lou Q, Xu K, Yan M, Xia H, Ma X, Yu X, Luo L. Alternative splicing complexity contributes to genetic improvement of drought resistance in the rice maintainer HuHan2B. Sci Rep 2017; 7:11686. [PMID: 28916800 PMCID: PMC5601427 DOI: 10.1038/s41598-017-12020-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
Water-saving and drought-resistantce rice (WDR) breeding practices have greatly increased grain yield and drought resistance. To study the genetic basis of adaptation to drought, transcriptome sequences from the WDR maintainer line HuHan2B and the recurrent parent HanFengB were analyzed for alternative splicing (AS) complexity. Intron retention, the dominant AS type, accounted for 42% of the observed AS events. Differential expression analysis revealed transcripts were preferentially expressed in different varieties and conditions. Based on gene ontology predictions, the biological functions of drought-induced transcripts were significantly enriched in genes involved in transcription regulation, chloroplast components and response to abiotic stimulus in HuHan2B, whereas developmental processes for reproduction were primarily enriched in HanFengB. The regulatory network of transcription factors was driven by cohorts of transcript splicing targets, resulting in more diversified regulatory relationships due to AS complexity than in our previous findings. Moreover, several genes were validated to accumulate novel splicing transcripts in a drought-induced manner. Together, these results suggest that HuHan2B and HanFengB share similar AS features but that a subset of genes with increased levels of AS involved in transcription regulatory networks may contribute an additional level of control for genetic improvement of drought resistance in rice maintainer HuHan2B through breeding.
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Affiliation(s)
- Haibin Wei
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | | | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China.
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36
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Evolutionarily Conserved Alternative Splicing Across Monocots. Genetics 2017; 207:465-480. [PMID: 28839042 DOI: 10.1534/genetics.117.300189] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splice-factor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
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Iñiguez LP, Ramírez M, Barbazuk WB, Hernández G. Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max. BMC Genomics 2017; 18:650. [PMID: 28830361 PMCID: PMC5568362 DOI: 10.1186/s12864-017-4054-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/11/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed. RESULTS We identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5'UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species. CONCLUSIONS The identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15-20 MY of divergence, and may point to the biological relevance of AS.
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Affiliation(s)
- Luis P. Iñiguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | | | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
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Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB. Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome. Mol Ecol Resour 2017; 17:1243-1256. [PMID: 28316149 DOI: 10.1111/1755-0998.12670] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 01/11/2023]
Abstract
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq™ data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq™ to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq™ platform provides better recovery on large transcripts, new gene locus identification and gene model correction. Reference-based AS detection with Iso-Seq™ data identifies AS within a higher fraction of multi-exonic genes than observed for published RNA-Seq analysis (45.8% vs. 37.5%). These data demonstrate that the Iso-Seq™ approach is useful for detecting AS events. Using the Iso-Seq-defined transcript collection in Amborella as a reference, we further describe a pipeline for detection of AS isoforms from PacBio Iso-Seq™ without using a reference sequence (de novo). Results using this pipeline show a 66%-76% overall success rate in identifying AS events. This de novoAS detection pipeline provides a method to accurately characterize and identify bona fide alternatively spliced transcripts in any nonmodel system that lacks a reference genome sequence. Hence, our pipeline has huge potential applications and benefits to the broader biology community.
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Affiliation(s)
- Xiaoxian Liu
- Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA
| | - Wenbin Mei
- Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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Fesenko I, Khazigaleeva R, Kirov I, Kniazev A, Glushenko O, Babalyan K, Arapidi G, Shashkova T, Butenko I, Zgoda V, Anufrieva K, Seredina A, Filippova A, Govorun V. Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens. Sci Rep 2017; 7:2698. [PMID: 28578384 PMCID: PMC5457400 DOI: 10.1038/s41598-017-02970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/20/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protoplasts. We identified 12 043 genes subject to alternative splicing and analyzed the extent to which AS contributes to proteome diversity. We could distinguish a few examples that unambiguously indicated the presence of two or more splice isoforms from the same locus at the proteomic level. Our results indicate that alternative isoforms have a small effect on proteome diversity. We also revealed that mRNAs and pre-mRNAs have thousands of complementary binding sites for long non-coding RNAs (lncRNAs) that may lead to potential interactions in transcriptome. This finding points to an additional level of gene expression and AS regulation by non-coding transcripts in Physcomitrella patens. Among the differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We found that treatment with abscisic (ABA) and methyl jasmonic acids (MeJA) led to an isoform-specific response and suggested that ABA in gametophores and MeJA in protoplasts regulate AS and the transcription of SR genes.
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Affiliation(s)
- Igor Fesenko
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Regina Khazigaleeva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kirov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Andrey Kniazev
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Glushenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Konstantin Babalyan
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Georgij Arapidi
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana Shashkova
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Ivan Butenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Ksenia Anufrieva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Seredina
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Filippova
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vadim Govorun
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
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40
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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Li Y, Dai C, Hu C, Liu Z, Kang C. Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:164-176. [PMID: 27997733 DOI: 10.1111/tpj.13462] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/23/2016] [Accepted: 12/14/2016] [Indexed: 05/21/2023]
Abstract
Alternative splicing (AS) is a key post-transcriptional regulatory mechanism, yet little information is known about its roles in fruit crops. Here, AS was globally analyzed in the wild strawberry Fragaria vesca genome with RNA-seq data derived from different stages of fruit development. The AS landscape was characterized and compared between the single-molecule, real-time (SMRT) and Illumina RNA-seq platform. While SMRT has a lower sequencing depth, it identifies more genes undergoing AS (57.67% of detected multiexon genes) when it is compared with Illumina (33.48%), illustrating the efficacy of SMRT in AS identification. We investigated different modes of AS in the context of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that of alternative acceptor sites (AA) is significantly increased post-fertilization when compared with pre-fertilization. When all the identified transcripts were combined, a total of 66.43% detected multiexon genes in strawberry undergo AS, some of which lead to a gain or loss of conserved domains in the gene products. The work demonstrates that SMRT sequencing is highly powerful in AS discovery and provides a rich data resource for later functional studies of different isoforms. Further, shifting AS modes may contribute to rapid changes of gene expression during fruit set.
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Affiliation(s)
- Yongping Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chungen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongchi Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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Jin L, Li G, Yu D, Huang W, Cheng C, Liao S, Wu Q, Zhang Y. Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae. BMC Genomics 2017; 18:130. [PMID: 28166730 PMCID: PMC5294800 DOI: 10.1186/s12864-017-3507-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/14/2017] [Indexed: 12/22/2022] Open
Abstract
Background Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. Results This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, using two different strains and multiple methods for cDNA library preparations. We identified alternatively spliced mRNA isoforms in over a half of the multi-exonic fungal genes. Over one-thousand isoforms involve TopHat novel splice junction; multiple types of combinatory alternative splicing patterns were identified. We showed that one Verticillium gene could use four different 5′ splice sites and two different 3′ donor sites to produce up to five mature mRNAs, representing one of the most sophisticated alternative splicing model in eukaryotes other than animals. Hundreds of novel intron types involving a pair of new splice sites were identified in the V. dahliae genome. All the types of AS events were validated by using RT-PCR. Functional enrichment analysis showed that AS genes are involved in most known biological functions and enriched in ATP biosynthesis, sexual/asexual reproduction, morphogenesis, signal transduction etc., predicting that the AS regulation modulates mRNA isoform output and shapes the V. dahliae proteome plasticity of the pathogen in response to the environmental and developmental changes. Conclusions These findings demonstrate the comprehensive alternative splicing mechanisms in a fungal plant pathogen, which argues the importance of this fungus in developing complicate genome regulation strategies in eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3507-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lirong Jin
- Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Guanglin Li
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.,College of Life Science, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Dazhao Yu
- Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China.
| | - Wei Huang
- Key Laboratory of Integrated Pest Management on Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Chao Cheng
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China
| | - Shengjie Liao
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.,Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China
| | - Qijia Wu
- Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.,Seqhealth Technology Co., Ltd, Wuhan, Hubei, 430075, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China. .,Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei, 430075, China.
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43
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Xiao GH, Wang K, Huang G, Zhu YX. Genome-scale analysis of the cotton KCS gene family revealed a binary mode of action for gibberellin A regulated fiber growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:577-89. [PMID: 26399709 PMCID: PMC5061104 DOI: 10.1111/jipb.12429] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/22/2015] [Indexed: 05/05/2023]
Abstract
Production of β-ketoacyl-CoA, which is catalyzed by 3-ketoacyl-CoA synthase (KCS), is the first step in very long chain fatty acid (VLCFA) biosynthesis. Here we identified 58 KCS genes from Gossypium hirsutum, 31 from G. arboreum and 33 from G. raimondii by searching the assembled cotton genomes. The gene family was divided into the plant-specific FAE1-type and the more general ELO-type. KCS transcripts were widely expressed and 32 of them showed distinct subgenome-specific expressions in one or more cotton tissues/organs studied. Six GhKCS genes rescued the lethality of elo2Δelo3Δ yeast double mutant, indicating that this gene family possesses diversified functions. Most KCS genes with GA-responsive elements (GAREs) in the promoters were significantly upregulated by gibberellin A3 (GA). Exogenous GA3 not only promoted fiber length, but also increased the thickness of cell walls significantly. GAREs present also in the promoters of several cellulose synthase (CesA) genes required for cell wall biosynthesis and they were all induced significantly by GA3 . Because GA treatment resulted in longer cotton fibers with thicker cell walls and higher dry weight per unit cell length, we suggest that it may regulate fiber elongation upstream of the VLCFA-ethylene pathway and also in the downstream steps towards cell wall synthesis.
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Affiliation(s)
- Guang-Hui Xiao
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Kun Wang
- Institute for Advanced Studies/College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gai Huang
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yu-Xian Zhu
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- Institute for Advanced Studies/College of Life Sciences, Wuhan University, Wuhan, 430072, China
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44
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Zhang C, Yang H, Yang H. Evolutionary Character of Alternative Splicing in Plants. Bioinform Biol Insights 2016; 9:47-52. [PMID: 26819552 PMCID: PMC4721685 DOI: 10.4137/bbi.s33716] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. What is the content rate of AS genes among the whole gene set? How many AS types are presented in the genome, and which type is dominant? How about the conservation ability of AS among different species? Which kinds of isoforms from some genes have the environmental response to help individual adaptation? Based on this background, we collected analysis results from 17 species to try to map out the landscape of AS studies in plants. We have noted the shortages of previous results, and we appeal to all scientists working in the AS field to make a standard protocol so that analyses between different projects are comparable.
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Affiliation(s)
- Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Hong Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Huizhao Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
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45
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Wei L, Cao X. The effect of transposable elements on phenotypic variation: insights from plants to humans. SCIENCE CHINA-LIFE SCIENCES 2016; 59:24-37. [PMID: 26753674 DOI: 10.1007/s11427-015-4993-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.
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Affiliation(s)
- Liya Wei
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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46
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Abstract
Allopolyploidy involves hybridization and duplication of divergent parental genomes and provides new avenues for gene expression. The expression levels of duplicated genes in polyploids can show deviation from parental additivity (the arithmetic average of the parental expression levels). Nonadditive expression has been widely observed in diverse polyploids and comprises at least three possible scenarios: (a) The total gene expression level in a polyploid is similar to that of one of its parents (expression-level dominance); (b) total gene expression is lower or higher than in both parents (transgressive expression); and (c) the relative contribution of the parental copies (homeologs) to the total gene expression is unequal (homeolog expression bias). Several factors may result in expression nonadditivity in polyploids, including maternal-paternal influence, gene dosage balance, cis- and/or trans-regulatory networks, and epigenetic regulation. As our understanding of nonadditive gene expression in polyploids remains limited, a new generation of investigators should explore additional phenomena (i.e., alternative splicing) and use other high-throughput "omics" technologies to measure the impact of nonadditive expression on phenotype, proteome, and metabolome.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525; , ,
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47
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Huang J, Gao Y, Jia H, Liu L, Zhang D, Zhang Z. Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement. BMC Genomics 2015; 16:363. [PMID: 25952680 PMCID: PMC4433066 DOI: 10.1186/s12864-015-1582-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/24/2015] [Indexed: 12/05/2022] Open
Abstract
Background Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement. Results In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 retained introns with transposable element (TE) sequences were detected in maize, which is far more than 9 retained introns with TEs detected in teosinte. This indicates that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3864 genes were significantly different between maize and teosinte. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes. Conclusions We suggest that both maize and teosinte share similar AS mechanisms, but more genes have increased AS complexity during domestication from teosinte to maize. Importantly, a subset of AS level-increased genes that encode transcription factors and stress-responsive proteins may have been selected during maize improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1582-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Youjun Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Dan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Collaborative Innovation Center for Grain Crops, Jingzhou, 434025, China.
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48
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Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium. Mol Genet Genomics 2014; 290:151-71. [DOI: 10.1007/s00438-014-0904-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
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