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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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2
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Yang H, Li P, Jin G, Gui D, Liu L, Zhang C. Temporal regulation of alternative splicing events in rice memory under drought stress. PLANT DIVERSITY 2022; 44:116-125. [PMID: 35281128 PMCID: PMC8897166 DOI: 10.1016/j.pld.2020.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
Plant adaptation to drought stress is essential for plant survival and crop yield. Recently, harnessing drought memory, which is induced by repeated stress and recovery cycles, was suggested as a means to improve drought resistance at the transcriptional level. However, the genetic mechanism underlying drought memory is unclear. Here, we carried out a quantitative analysis of alternative splicing (AS) events in rice memory under drought stress, generating 12 transcriptome datasets. Notably, we identified exon skipping (ES) as the predominant AS type (>80%) in differential alternative splicing (DAS) in response to drought stress. Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94% to 60.70% depending on the species, suggesting that the relative frequency of DAS types in plants is likely to be species-specific. The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC. Since U12-type splicing uses the AT-AC site, this suggests that drought stress may increase U12-type splicing, and thus increase ES frequency. We hypothesize that multiple isoforms derived from exon skipping may be induced by drought stress in rice. We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.
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Affiliation(s)
- Hong Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Li Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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3
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Yu K, Feng M, Yang G, Sun L, Qin Z, Cao J, Wen J, Li H, Zhou Y, Chen X, Peng H, Yao Y, Hu Z, Guo W, Sun Q, Ni Z, Adams K, Xin M. Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat. PLANT PHYSIOLOGY 2020; 184:1955-1968. [PMID: 33051269 PMCID: PMC7723095 DOI: 10.1104/pp.20.00773] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/04/2020] [Indexed: 05/23/2023]
Abstract
Alternative splicing (AS) occurs extensively in eukaryotes as an important mechanism for regulating transcriptome complexity and proteome diversity, but variation in the AS landscape in response to domestication and polyploidization in crops is unclear. Hexaploid wheat (AABBDD, Triticum aestivum) has undergone two separate allopolyploidization events, providing an ideal model for studying AS changes during domestication and polyploidization events. In this study, we performed high-throughput transcriptome sequencing of roots and leaves from wheat species with varied ploidies, including wild diploids (AbAb, Triticum boeoticum) and tetraploids (AABB, Triticum dicoccoides), domesticated diploids (AmAm, Triticum monococcum) and tetraploids (AABB, Triticum dicoccum), hexaploid wheat (AABBDD, T aestivum), as well as newly synthesized hexaploids together with their parents. Approximately 22.1% of genes exhibited AS, with the major AS type being intron retention. The number of AS events decreased after domestication in both diploids and tetraploids. Moreover, the frequency of AS occurrence tended to decrease after polyploidization, consistent with the functional sharing model that proposes AS and duplicated genes are complementary in regulating transcriptome plasticity in polyploid crops. In addition, the subgenomes exhibited biased AS responses to polyploidization, and ∼87.1% of homeologs showed AS partitioning in hexaploid wheat. Interestingly, substitution of the D-subgenome modified 42.8% of AS patterns of the A- and B-subgenomes, indicating subgenome interplay reprograms AS profiles at a genome-wide level, although the causal-consequence relationship requires further study. Conclusively, our study shows that AS variation occurs extensively after polyploidization and domestication in wheat species.
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Affiliation(s)
- Kuohai Yu
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Man Feng
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Guanghui Yang
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lv Sun
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Cao
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jingjing Wen
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Haoran Li
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yan Zhou
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiangping Chen
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Keith Adams
- Botany Department, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Mingming Xin
- Key Laboratory of Crop Heterosis Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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Sellamuthu G, Jegadeeson V, Sajeevan RS, Rajakani R, Parthasarathy P, Raju K, Shabala L, Chen ZH, Zhou M, Sowdhamini R, Shabala S, Venkataraman G. Distinct Evolutionary Origins of Intron Retention Splicing Events in NHX1 Antiporter Transcripts Relate to Sequence Specific Distinctions in Oryza Species. FRONTIERS IN PLANT SCIENCE 2020; 11:267. [PMID: 32218795 PMCID: PMC7078337 DOI: 10.3389/fpls.2020.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/20/2020] [Indexed: 05/30/2023]
Abstract
The genome of Asian cultivated rice (Oryza sativa L.) shows the presence of six organelle-specific and one plasma membrane (OsNHX1-7) NHX-type cation proton antiporters. Of these, vacuolar-localized OsNHX1 is extensively characterized. The genus Oryza consists of 27 species and 11 genome-types, with cultivated rice, diploid O. sativa, having an AA-type genome. Oryza NHX1 orthologous regions (gene organization, 5' upstream cis elements, amino acid residues/motifs) from closely related Oryza AA genomes cluster distinctly from NHX1 regions from more ancestral Oryza BB, FF and KKLL genomes. These sequence-specific distinctions also extend to two separate intron retention (IR) events involving Oryza NHX1 transcripts that occur at the 5' and 3' ends of the NHX1 transcripts. We demonstrate that the IR event involving the 5' UTR is present only in more recently evolved Oryza AA genomes while the IR event governing retention of the 13th intron of Oryza NHX1 (terminal intron) is more ancient in origin, also occurring in halophytic wild rice, Oryza coarctata (KKLL). We also report presence of a retro-copy of the OcNHX1 cDNA in the genome of O. coarctata (rOcNHX1). Preferential species and tissue specific up- or down-regulation of the correctly spliced NHX1 transcript/5' UTR/13th intron-retaining splice variants under salinity was observed. The implications of IR on NHX1 mRNA stability and ORF diversity in Oryza spp. is discussed.
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Affiliation(s)
| | - Vidya Jegadeeson
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, Chennai, India
| | - Radha Sivarajan Sajeevan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Raja Rajakani
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, Chennai, India
| | - Pavithra Parthasarathy
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, Chennai, India
| | - Kalaimani Raju
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, Chennai, India
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS, Australia
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS, Australia
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS, Australia
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, Chennai, India
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6
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Li L, Wang F, Li X, Peng Y, Zhang H, Hey S, Wang G, Wang J, Gu R. Comparative analysis of the accelerated aged seed transcriptome profiles of two maize chromosome segment substitution lines. PLoS One 2019; 14:e0216977. [PMID: 31710606 PMCID: PMC6844465 DOI: 10.1371/journal.pone.0216977] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Seed longevity is one of the most essential characteristics of seed quality. Two chromosome segment substitution lines, I178 and X178, which show significant differences in seed longevity, were subjected to transcriptome sequencing before and after five days of accelerated aging (AA) treatments. Compared to the non-aging treatment, 286 and 220 differentially expressed genes (DEGs) were identified after 5 days of aging treatment in I178 and X178, respectively. Of these DEGs, 98 were detected in both I178 and X178, which were enriched in Gene Ontology (GO) terms of the cellular component of the nuclear part, intracellular part, organelle and membrane. Only 86 commonly downregulated genes were enriched in GO terms of the carbohydrate derivative catabolic process. Additionally, transcriptome analysis of alternative splicing (AS) events in I178 and X178 showed that 63.6% of transcript isoforms occurred AS in all samples, and only 1.6% of transcript isoforms contained 169 genes that exhibited aging-specific AS arising after aging treatment. Combined with the reported QTL mapping result, 7 DEGs exhibited AS after aging treatment, and 13 DEGs in mapping interval were potential candidates that were directly or indirectly related to seed longevity.
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Affiliation(s)
- Li Li
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Feng Wang
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xuhui Li
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yixuan Peng
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Stefan Hey
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wang
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (JW); (RG)
| | - Riliang Gu
- Seed Science and Technology Research Center, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory for Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (JW); (RG)
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Hybrid Sequencing of Full-Length cDNA Transcripts of the Medicinal Plant Scutellaria baicalensis. Int J Mol Sci 2019; 20:ijms20184426. [PMID: 31505762 PMCID: PMC6770217 DOI: 10.3390/ijms20184426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/28/2019] [Accepted: 09/04/2019] [Indexed: 11/17/2022] Open
Abstract
Scutellaria baicalensis is a well-known medicinal plant that produces biologically active flavonoids, such as baicalin, baicalein, and wogonin. Pharmacological studies have shown that these compounds have anti-inflammatory, anti-bacterial, and anti-cancer activities. Therefore, it is of great significance to investigate the genetic information of S. baicalensis, particularly the genes related to the biosynthetic pathways of these compounds. Here, we constructed the full-length transcriptome of S. baicalensis using a hybrid sequencing strategy and acquired 338,136 full-length sequences, accounting for 93.3% of the total reads. After the removal of redundancy and correction with Illumina short reads, 75,785 nonredundant transcripts were generated, among which approximately 98% were annotated with significant hits in the protein databases, and 11,135 sequences were classified as lncRNAs. Differentially expressed gene (DEG) analysis showed that most of the genes related to flavonoid biosynthesis were highly expressed in the roots, consistent with previous reports that the flavonoids were mainly synthesized and accumulated in the roots of S. baicalensis. By constructing unique transcription models, a total of 44,071 alternative splicing (AS) events were identified, with intron retention (IR) accounting for the highest proportion (44.5%). A total of 94 AS events were present in five key genes related to flavonoid biosynthesis, suggesting that AS may play important roles in the regulation of flavonoid biosynthesis in S. baicalensis. This study provided a large number of highly accurate full-length transcripts, which represents a valuable genetic resource for further research of the molecular biology of S. baicalensis, such as the development, breeding, and biosynthesis of active ingredients.
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Bedre R, Irigoyen S, Petrillo E, Mandadi KK. New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. FRONTIERS IN PLANT SCIENCE 2019; 10:740. [PMID: 31231413 PMCID: PMC6558643 DOI: 10.3389/fpls.2019.00740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, United States
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, United States
| | - Ezequiel Petrillo
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Weslaco, TX, United States
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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9
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Rodionov AV, Amosova AV, Belyakov EA, Zhurbenko PM, Mikhailova YV, Punina EO, Shneyer VS, Loskutov IG, Muravenko OV. Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Phule AS, Barbadikar KM, Maganti SM, Seguttuvel P, Subrahmanyam D, Babu MBBP, Kumar PA. RNA-seq reveals the involvement of key genes for aerobic adaptation in rice. Sci Rep 2019; 9:5235. [PMID: 30918284 PMCID: PMC6437204 DOI: 10.1038/s41598-019-41703-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/01/2019] [Indexed: 12/24/2022] Open
Abstract
Adaptation of rice to the aerobic condition is needed to cope with the water scarcity as well as to ensure sustainable yield in future. To understand the molecular mechanisms responsible for aerobic adaptation in rice, we performed RNA-seq analysis of root and shoot i.e. developing panicle tissues at panicle initiation stage in two cultivars adapted to aerobic (CR Dhan 202) and traditional transplanted anaerobic (BPT 5204) conditions. The RNA-seq data emanated from 1.65 billion clean reads with approximately 37 million reads per sample. The number of differentially expressed transcripts was higher in the root than that in the shoot under both aerobic and anaerobic conditions. The transcription factors viz. MADS4, MADS5, MADS6, MADS7, MADS15 and transporters involved in sugar (SWEET3A) and nutrient uptake (PHT1;6, MDR-like ABC and vacuolar iron transporter homolog 2) were highly and uniquely expressed in the aerobic adapted cultivar (AAC) CR Dhan 202 under aerobic condition indicating their role in adaptation. The hormones such as ethylene and abscisic acid might be significantly involved in imparting aerobic adaptation. The higher expression of root related genes in the AAC under aerobic conditions suggests the involvement and sensitivity of roots to the water limiting condition. The metabolic activities are also more pronounced in the roots which impart rigorous plant establishment under the aerobic condition. The presence of alternative splice variants in the transcripts viz. Tetratrico peptide repeat (TPR) domain containing protein and GOLDEN2-LIKE1 (GLK1) additionally confirms that post transcriptional regulation is also crucial for aerobic adaptation. The QTLs related to root traits and stress tolerance harboring the uniquely expressed genes, which were identified in the present study can be deployed in molecular breeding programs to develop elite, high yielding aerobic rice cultivars.
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Affiliation(s)
- Amol S Phule
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Hyderabad, 30, India
| | - Kalyani M Barbadikar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Sheshu Madhav Maganti
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - P Seguttuvel
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - D Subrahmanyam
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - M B B Prasad Babu
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Polumetla A Kumar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India.
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11
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Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3 (BETHESDA, MD.) 2019; 9:755-767. [PMID: 30642874 PMCID: PMC6404599 DOI: 10.1534/g3.118.201008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
Abstract
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA
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12
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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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13
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Grau-Bové X, Ruiz-Trillo I, Irimia M. Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Genome Biol 2018; 19:135. [PMID: 30223879 PMCID: PMC6142364 DOI: 10.1186/s13059-018-1499-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022] Open
Abstract
Background Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode across non-animal eukaryotes, animals have unusually high rates of exon skipping. However, when and how this high prevalence of exon skipping evolved is unknown. Since exon skipping can greatly expand proteomes, answering these questions sheds light on the evolution of higher organismal complexity in metazoans. Results We used RNA-seq data to quantify exon skipping and intron retention frequencies across 65 eukaryotic species, with particular focus on early branching animals and unicellular holozoans. We found that only bilaterians have significantly increased their exon skipping frequencies compared to all other eukaryotic groups. Unlike in other eukaryotes, however, exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving sequences, suggesting that exon skipping involvement in proteome expansion predated the increase in frequency. We also identified architectural features consistently associated with higher exon skipping rates within all studied eukaryotic genomes. Remarkably, these architectures became more prevalent during animal evolution, indicating co-evolution between genome architectures and exon skipping frequencies. Conclusion We suggest that the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes. Electronic supplementary material The online version of this article (10.1186/s13059-018-1499-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. .,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain. .,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
| | - Manuel Irimia
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10-12, 08002, Barcelona, Catalonia, Spain.
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14
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Sun Y, Hou H, Song H, Lin K, Zhang Z, Hu J, Pang E. The comparison of alternative splicing among the multiple tissues in cucumber. BMC PLANT BIOLOGY 2018; 18:5. [PMID: 29301488 PMCID: PMC5755334 DOI: 10.1186/s12870-017-1217-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored. RESULTS To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts. CONCLUSIONS Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.
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Affiliation(s)
- Ying Sun
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Han Hou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao, 266101 China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jinglu Hu
- Graduate School of Information, Production and Systems, Waseda University, Kitakyushu-shi, 808-0135 Japan
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
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15
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Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0474. [PMID: 27994117 DOI: 10.1098/rstb.2015.0474] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Lu Chen
- West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, People's Republic of China
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK .,Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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16
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Zhang SJ, Wang C, Yan S, Fu A, Luan X, Li Y, Sunny Shen Q, Zhong X, Chen JY, Wang X, Chin-Ming Tan B, He A, Li CY. Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. Mol Biol Evol 2017; 34:2453-2468. [PMID: 28957512 PMCID: PMC5850651 DOI: 10.1093/molbev/msx212] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent RNA-seq technology revealed thousands of splicing events that are under rapid evolution in primates, whereas the reliability of these events, as well as their combination on the isoform level, have not been adequately addressed due to its limited sequencing length. Here, we performed comparative transcriptome analyses in human and rhesus macaque cerebellum using single molecule long-read sequencing (Iso-seq) and matched RNA-seq. Besides 359 million RNA-seq reads, 4,165,527 Iso-seq reads were generated with a mean length of 14,875 bp, covering 11,466 human genes, and 10,159 macaque genes. With Iso-seq data, we substantially expanded the repertoire of alternative RNA processing events in primates, and found that intron retention and alternative polyadenylation are surprisingly more prevalent in primates than previously estimated. We then investigated the combinatorial mode of these alternative events at the whole-transcript level, and found that the combination of these events is largely independent along the transcript, leading to thousands of novel isoforms missed by current annotations. Notably, these novel isoforms are selectively constrained in general, and 1,119 isoforms have even higher expression than the previously annotated major isoforms in human, indicating that the complexity of the human transcriptome is still significantly underestimated. Comparative transcriptome analysis further revealed 502 genes encoding selectively constrained, lineage-specific isoforms in human but not in rhesus macaque, linking them to some lineage-specific functions. Overall, we propose that the independent combination of alternative RNA processing events has contributed to complex isoform evolution in primates, which provides a new foundation for the study of phenotypic difference among primates.
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Affiliation(s)
- Shi-Jian Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Chenqu Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Science, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shouyu Yan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Aisi Fu
- Wuhan Institute of Biotechnology, Wuhan, Hubei, China
| | - Xuke Luan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Science, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yumei Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiaoming Zhong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences College of Medicine, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chuan-Yun Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
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17
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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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18
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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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19
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Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Res 2017; 27:885-896. [PMID: 28420692 PMCID: PMC5411782 DOI: 10.1101/gr.217117.116] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/14/2017] [Indexed: 01/16/2023]
Abstract
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Tom Barker
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | - Fu-Hao Lu
- John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | | | - Dina Raats
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | | | | | - Ned Peel
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | | | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Guotai Yu
- John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Dan M Bolser
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Guy Namaati
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Arnaud Kerhornou
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Robert P Davey
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - Federica Di Palma
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley Western Australia 6009, Australia
| | - Paul J Kersey
- EMBL European Bioinformatics Institute, Hinxton, CB10 1SD, United Kingdom
| | | | - Ksenia V Krasileva
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- The Sainsbury Laboratory, Norwich, NR4 7UH, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | | | - Matthew D Clark
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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20
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Collu G, Farci D, Esposito F, Pintus F, Kirkpatrick J, Piano D. New insights into the operative network of FaEO, an enone oxidoreductase from Fragaria x ananassa Duch. PLANT MOLECULAR BIOLOGY 2017; 94:125-136. [PMID: 28283921 DOI: 10.1007/s11103-017-0597-5] [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: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
The 2-methylene-furan-3-one reductase or Fragaria x ananassa Enone Oxidoreductase (FaEO) catalyses the last reductive step in the biosynthesis of 4-hydroxy-2,5-dimethyl-3(2H)-furanone, a major component in the characteristic flavour of strawberries. In the present work, we describe the association between FaEO and the vacuolar membrane of strawberry fruits. Even if FaEO lacks epitopes for stable or transient membrane-interactions, it contains a calmodulin-binding region, suggesting that in vivo FaEO may be associated with the membrane via a peripheral protein complex with calmodulin. Moreover, we also found that FaEO occurs in dimeric form in vivo and, as frequently observed for calmodulin-regulated proteins, it may be expressed in different isoforms by alternative gene splicing. Further mass spectrometry analysis confirmed that the isolated FaEO consists in the already known isoform and that it is the most characteristic during ripening. Finally, a characterization by absorption spectroscopy showed that FaEO has specific flavoprotein features. The relevance of these findings and their possible physiological implications are discussed.
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Affiliation(s)
- Gabriella Collu
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 52175, Bonn, Germany
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, Italy
| | - Francesca Pintus
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, Italy
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutebergstraβe 11, 07745, Jena, Germany
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy.
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21
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Iñiguez LP, Hernández G. The Evolutionary Relationship between Alternative Splicing and Gene Duplication. Front Genet 2017; 8:14. [PMID: 28261262 PMCID: PMC5306129 DOI: 10.3389/fgene.2017.00014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/02/2017] [Indexed: 01/23/2023] Open
Abstract
The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study.
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Affiliation(s)
- Luis P Iñiguez
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
| | - Georgina Hernández
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
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22
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Ramírez-Sánchez O, Pérez-Rodríguez P, Delaye L, Tiessen A. Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins. GENOMICS, PROTEOMICS & BIOINFORMATICS 2016; 14:357-370. [PMID: 27998811 PMCID: PMC5200936 DOI: 10.1016/j.gpb.2016.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 01/27/2023]
Abstract
Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.
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Affiliation(s)
- Obed Ramírez-Sánchez
- Genetic Engineering Department, CINVESTAV Unidad Irapuato, Irapuato, CP 36821, Mexico
| | | | - Luis Delaye
- Genetic Engineering Department, CINVESTAV Unidad Irapuato, Irapuato, CP 36821, Mexico
| | - Axel Tiessen
- Genetic Engineering Department, CINVESTAV Unidad Irapuato, Irapuato, CP 36821, Mexico.
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23
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Chaudhary PR, Bang H, Jayaprakasha GK, Patil BS. Variation in Key Flavonoid Biosynthetic Enzymes and Phytochemicals in 'Rio Red' Grapefruit (Citrus paradisi Macf.) during Fruit Development. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:9022-9032. [PMID: 27808514 DOI: 10.1021/acs.jafc.6b02975] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the current study, the phytochemical contents and expression of genes involved in flavonoid biosynthesis in Rio Red grapefruit were studied at different developmental and maturity stages for the first time. Grapefruit were harvested in June, August, November, January, and April and analyzed for the levels of carotenoids, vitamin C, limonoids, flavonoids, and furocoumarins by HPLC. In addition, genes encoding for phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), and 1,2-rhamnosyltransferase (2RT) were isolated, and their expression in grapefruit juice vesicles was studied. Fruit maturity had significant influence on the expression of the genes, with PAL, CHS, and CHI having higher expression in immature fruits (June), whereas 2RT expression was higher in mature fruits (November and January). The levels of flavonoids (except naringin and poncirin), vitamin C, and furocoumarins gradually decreased from June to April. Furthermore, limonin levels sharply decreased in January. Lycopene decreased whereas β-carotene gradually increased with fruit maturity. Naringin did not exactly follow the pattern of 2RT or of PAL, CHS, and CHI expression, indicating that the four genes may have complementary effects on the level of naringin. Nevertheless, of the marketable fruit stages, early-season grapefruits harvested in November contained more beneficial phytochemicals as compared to mid- and late-season fruits harvested in January and April, respectively.
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Affiliation(s)
- Priyanka R Chaudhary
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
| | - Haejeen Bang
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
| | | | - Bhimanagouda S Patil
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University , College Station, Texas 77845, United States
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24
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Han B, Gu J, Zhao L, Guo H, Xie Y, Zhao S, Song X, Han L, Liu L. Factors Affecting the Radiosensitivity of Hexaploid Wheat to γ-Irradiation: Radiosensitivity of Hexaploid Wheat (Triticum aestivum L.) [Corrected]. PLoS One 2016; 11:e0161700. [PMID: 27551965 PMCID: PMC4995049 DOI: 10.1371/journal.pone.0161700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/10/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding the radiosensitivity of plants, an important factor in crop mutation breeding programs, requires a thorough investigation of the factors that contribute to this trait. In this study, we used the highly radiosensitive wheat (Triticum aestivum L.) variety HY1 and J411, a γ-irradiation-insensitive control, which were screened from a natural population, to examine the factors affecting radiosensitivity, including free radical content and total antioxidant capacity, as well as the expression of TaKu70 and TaKu80 (DNA repair-related genes) as measured by real-time PCR. We also investigated the alternative splicing of this gene in the wild-type wheat ecotype by sequence analysis. Free radical contents and total antioxidant capacity significantly increased upon exposure of HY1 wheat to γ-irradiation in a dose-dependent manner. By contrast, in J411, the free radical contents exhibited a similar trend, but the total antioxidant capacity exhibited a downward trend upon increasing γ-irradiation. Additionally, we detected dose-dependent increases in TaKu70 and TaKu80 expression levels in γ-irradiated HY1, while in J411, TaKu70 expression levels increased, followed by a decline. We also detected alternative splicing of TaKu70 mRNA, namely, intron retention, in HY1 but not in J411. Our findings indicate that γ-irradiation induces oxidative stress and DNA damage in hexaploid wheat, resulting in growth retardation of seedlings, and they suggest that TaKu70 may play a causal role in radiosensitivity in HY1. Further studies are required to exploit these factors to improve radiosensitivity in other wheat varieties.
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Affiliation(s)
- Bing Han
- Academy of Life Science, Qingdao Agricultural University, Qingdao, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Xiyun Song
- Academy of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences /National Key Facility for Crop Gene Resources and Genetic Improvement /National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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