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Yan X, Bai D, Song H, Lin K, Pang E. Alternative splicing during fruit development among fleshy fruits. BMC Genomics 2021; 22:762. [PMID: 34702184 PMCID: PMC8547070 DOI: 10.1186/s12864-021-08111-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/20/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. RESULTS We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96-17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. CONCLUSIONS We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.
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Affiliation(s)
- Xiaomin Yan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Dan Bai
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and 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 and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and 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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Yang J, Lv W, Shao L, Fu Y, Liu H, Yang C, Chen A, Xie X, Wang Z, Li C. PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species. FRONTIERS IN PLANT SCIENCE 2021; 12:737004. [PMID: 34691113 PMCID: PMC8529222 DOI: 10.3389/fpls.2021.737004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/02/2021] [Indexed: 06/04/2023]
Abstract
In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.
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Affiliation(s)
- Jingli Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Wanqiu Lv
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Haimei Liu
- Biology Group, Jiamusi No.1 High School, Jiamusi, China
| | - Chengjun Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Aihua Chen
- Economic Forest Laboratory, Mudanjiang Branch of Heilongjiang Academy of Forestry, Mudanjiang, China
| | - Xieyu Xie
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Zhiwei Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
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Wei S, Xia R, Chen C, Shang X, Ge F, Wei H, Chen H, Wu Y, Xie Q. ZmbHLH124 identified in maize recombinant inbred lines contributes to drought tolerance in crops. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2069-2081. [PMID: 34031958 PMCID: PMC8486247 DOI: 10.1111/pbi.13637] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 03/28/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Due to climate change, drought has become a severe abiotic stress that affects the global production of all crops. Elucidation of the complex physiological mechanisms underlying drought tolerance in crops will support the cultivation of new drought-tolerant crop varieties. Here, two drought-tolerant lines, RIL70 and RIL73, and two drought-sensitive lines, RIL44 and RIL93, from recombinant inbred lines (RIL) generated from maize drought-tolerant line PH4CV and drought-sensitive line F9721, were selected for a comparative RNA-seq study. Through transcriptome analyses, we found that gene expression differences existed between drought-tolerant and -sensitive lines, but also differences between the drought-tolerant lines, RIL70 and RIL73. ZmbHLH124 in RIL73, named as ZmbHLH124T-ORG which origins from PH4CV and encodes a bHLH type transcription factor, was specifically up-regulated during drought stress. In addition, we identified a substitution in ZmbHLH124 that produced an early stop codon in sensitive lines (ZmbHLH124S-ORG ). Overexpression of ZmbHLH124T-ORG , but not ZmbHLH124S-ORG , in maize and rice enhanced plant drought tolerance and up-regulated the expression of drought-responsive genes. Moreover, we found that ZmbHLH124T-ORG could directly bind the cis-acting elements in ZmDREB2A promoter to enhance its expression. Taken together, this work identified a valuable genetic locus and provided a new strategy for breeding drought-tolerant crops.
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Affiliation(s)
- Shaowei Wei
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Xia
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Chengxuan Chen
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoling Shang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Fengyong Ge
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Huimin Wei
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Huabang Chen
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaorong Wu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Qi Xie
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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54
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Golicz AA, Allu AD, Li W, Lohani N, Singh MB, Bhalla PL. A dynamic intron retention program regulates the expression of several hundred genes during pollen meiosis. PLANT REPRODUCTION 2021; 34:225-242. [PMID: 34019149 DOI: 10.1007/s00497-021-00411-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/19/2021] [Indexed: 05/12/2023]
Abstract
Intron retention is a stage-specific mechanism of functional attenuation of a subset of co-regulated, functionally related genes during early stages of pollen development. To improve our understanding of the gene regulatory mechanisms that drive developmental processes, we performed a genome-wide study of alternative splicing and isoform switching during five key stages of pollen development in field mustard, Brassica rapa. Surprisingly, for several hundred genes (12.3% of the genes analysed), isoform switching results in stage-specific expression of intron-retaining transcripts at the meiotic stage of pollen development. In such cases, we report temporally regulated switching between expression of a canonical, translatable isoform and an intron-retaining transcript that is predicted to produce a truncated and presumably inactive protein. The results suggest a new pervasive mechanism underlying modulation of protein levels in a plant developmental program. The effect is not based on gene expression induction but on the type of transcript produced. We conclude that intron retention is a stage-specific mechanism of functional attenuation of a subset of co-regulated, functionally related genes during meiosis, especially genes related to ribosome biogenesis, mRNA transport and nuclear envelope architecture. We also propose that stage-specific expression of a non-functional isoform of Brassica rapa BrSDG8, a non-redundant member of histone methyltransferase gene family, linked to alternative splicing regulation, may contribute to the intron retention observed.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Annapurna D Allu
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Wei Li
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
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55
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Chen S, Ren C, Zhai J, Yu J, Zhao X, Li Z, Zhang T, Ma W, Han Z, Ma C. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. Brief Bioinform 2021; 21:676-686. [PMID: 30815667 PMCID: PMC7299299 DOI: 10.1093/bib/bbz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, resulting in the loss of significant biological information and insights. To fill this gap, we present Comprehensive Assembly and Functional annotation of Unmapped RNA-Seq data (CAFU), a Galaxy-based framework that can facilitate the large-scale analysis of unmapped RNA sequencing (RNA-Seq) reads from single- and mixed-species samples. By taking advantage of machine learning techniques, CAFU addresses the issue of accurately identifying the species origin of transcripts assembled using unmapped reads from mixed-species samples. CAFU also represents an innovation in that it provides a comprehensive collection of functions required for transcript confidence evaluation, coding potential calculation, sequence and expression characterization and function annotation. These functions and their dependencies have been integrated into a Galaxy framework that provides access to CAFU via a user-friendly interface, dramatically simplifying complex exploration tasks involving unmapped RNA-Seq reads. CAFU has been validated with RNA-Seq data sets from wheat and Zea mays (maize) samples. CAFU is freely available via GitHub: https://github.com/cma2015/CAFU.
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Affiliation(s)
- Siyuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chengzhi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Jiantao Yu
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Xuyang Zhao
- College of Information Engineering, Northwest Agriculture and Forestry University
| | - Zelong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Wenlong Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest Agriculture and Forestry University
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56
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Li H, Li A, Shen W, Ye N, Wang G, Zhang J. Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation. RICE (NEW YORK, N.Y.) 2021; 14:75. [PMID: 34383135 PMCID: PMC8360254 DOI: 10.1186/s12284-021-00516-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/03/2021] [Indexed: 05/14/2023]
Abstract
Alternative splicing is a widespread phenomenon, which generates multiple isoforms of the gene product. Reproductive development is the key process for crop production. Although numerous forms of alternative splicing have been identified in model plants, large-scale study of alternative splicing dynamics during reproductive development in rice has not been conducted. Here, we investigated alternative splicing of reproductive development of young panicles (YP), unfertilized florets (UF) and fertilized florets (F) in rice using direct RNA sequencing, small RNA sequencing, and degradome sequencing. We identified a total of 35,317 alternative splicing (AS) events, among which 67.2% splicing events were identified as novel alternative splicing events. Intron retention (IR) was the most abundant alternative splicing subtype. Splicing factors that differentially expressed and alternatively spliced could result in global alternative splicing. Global analysis of miRNAs-targets prediction revealed that alternative spliced transcripts affected miRNAs' targets during development. Degradome sequencing detected only 6.8% of the differentially alternative splicing transcripts, suggesting a productive transcripts generation during development. In addition, alternative splicing isoforms of Co-like, a transcription factor, interacted with Casein kinase 1-like protein HD1 (CKI) examined in luciferase assay, which could modulate normal male-floral organs development and flowering time. These results reveal that alternative splicing is intensely associated with developmental stages, and a high complexity of gene regulation.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Aixuan Li
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Shen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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57
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Gao P, Quilichini TD, Zhai C, Qin L, Nilsen KT, Li Q, Sharpe AG, Kochian LV, Zou J, Reddy AS, Wei Y, Pozniak C, Patterson N, Gillmor CS, Datla R, Xiang D. Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1624-1643. [PMID: 33706417 PMCID: PMC8384600 DOI: 10.1111/pbi.13579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat crops are poorly understood. To address this knowledge gap, we developed a pipeline for the analysis of alternatively spliced transcript isoforms, which takes the high sequence similarity among polyploid wheat subgenomes into account. Through analysis of synteny and detection of collinearity of homoeologous subgenomes, conserved and specific AS events across five wheat and grass species were identified. A global analysis of the regulation of AS in diploid grass and polyploid wheat grains revealed diversity in AS events not only between the endosperm, pericarp and embryo overdevelopment, but also between subgenomes. Analysis of AS in homoeologous triads of polyploid wheats revealed evolutionary divergence between gene-level and transcript-level regulation of embryogenesis. Evolutionary age analysis indicated that the generation of novel transcript isoforms has occurred in young genes at a more rapid rate than in ancient genes. These findings, together with the development of comprehensive AS resources for wheat and grass species, advance understanding of the evolution of regulatory features of AS during embryogenesis and grain development in wheat.
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Affiliation(s)
- Peng Gao
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Teagen D. Quilichini
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Chun Zhai
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Li Qin
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Kirby T. Nilsen
- Agriculture and Agri‐Food CanadaBrandon Research and Development CentreBrandonMBCanada
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Andrew G. Sharpe
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Leon V. Kochian
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Jitao Zou
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Anireddy S.N. Reddy
- Department of Biology and Program in Cell and Molecular BiologyColorado State UniversityFort CollinsCOUSA
| | - Yangdou Wei
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSKCanada
| | - Nii Patterson
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)Unidad de Genómica AvanzadaCentro de Investigación y Estudios Avanzados del IPN (CINVESTAV‐IPN)IrapuatoGuanajuatoMexico
| | - Raju Datla
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
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PID: An integrative and comprehensive platform of plant intron. Comput Biol Chem 2021; 93:107528. [PMID: 34111777 DOI: 10.1016/j.compbiolchem.2021.107528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/07/2020] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
Intron is a non-coding sequence of a broken gene and participates in important biological processes, such as transcription regulation, alternative splicing, and nuclear export. With the development of plant genomes, a comprehensive platform for intron analysis in plants must be established. Plant Intron Database (PID), a publicly available searchable database, was developed to efficiently store, query, analyze, and integrate intron resources in plants. The information of intron, exon, and gene can be searched by key words in PID. Users cannot only view intron length distribution pie chart and 5' and 3' splice site sequence feature maps in a statistical interface but can also browse intron information in a graphical visualization interface through JBrowse. ViroBlast for sequence homology searches, Intron detection and sequence interception tools were also provided. PID contains annotated genes from 118 sequenced plants, 24,782,048 introns, 30,843,049 exons, and 414 visual maps. This tool will greatly accelerate research on the distribution, length characteristics, and functions of introns in plants. PID is accessible at http://biodb.sdau.edu.cn/PID/index.php.
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Li Z, Tang J, Bassham DC, Howell SH. Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize. PLANT PHYSIOLOGY 2021; 186:1318-1335. [PMID: 33705553 PMCID: PMC8195531 DOI: 10.1093/plphys/kiab110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/18/2021] [Indexed: 05/04/2023]
Abstract
Elevated temperatures enhance alternative RNA splicing in maize (Zea mays) with the potential to expand the repertoire of plant responses to heat stress. Alternative RNA splicing generates multiple RNA isoforms for many maize genes, and here we observed changes in the pattern of RNA isoforms with temperature changes. Increases in maximum daily temperature elevated the frequency of the major modes of alternative splices (AS), in particular retained introns and skipped exons. The genes most frequently targeted by increased AS with temperature encode factors involved in RNA processing and plant development. Genes encoding regulators of alternative RNA splicing were themselves among the principal AS targets in maize. Under controlled environmental conditions, daily changes in temperature comparable to field conditions altered the abundance of different RNA isoforms, including the RNAs encoding the splicing regulator SR45a, a member of the SR45 gene family. We established an "in protoplast" RNA splicing assay to show that during the afternoon on simulated hot summer days, SR45a RNA isoforms were produced with the potential to encode proteins efficient in splicing model substrates. With the RNA splicing assay, we also defined the exonic splicing enhancers that the splicing-efficient SR45a forms utilize to aid in the splicing of model substrates. Hence, with rising temperatures on hot summer days, SR45a RNA isoforms in maize are produced with the capability to encode proteins with greater RNA splicing potential.
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Affiliation(s)
- Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
| | - Jie Tang
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Diane C Bassham
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Stephen H. Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
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Butt H, Bazin J, Alshareef S, Eid A, Benhamed M, Reddy ASN, Crespi M, Mahfouz MM. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation. Commun Biol 2021; 4:529. [PMID: 33953336 PMCID: PMC8100303 DOI: 10.1038/s42003-021-02051-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1GEX1ARESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants. Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jeremie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Sahar Alshareef
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Moussa Benhamed
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, King Abdullah, University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Matallana-Ramirez LP, Whetten RW, Sanchez GM, Payn KG. Breeding for Climate Change Resilience: A Case Study of Loblolly Pine ( Pinus taeda L.) in North America. FRONTIERS IN PLANT SCIENCE 2021; 12:606908. [PMID: 33995428 PMCID: PMC8119900 DOI: 10.3389/fpls.2021.606908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 05/25/2023]
Abstract
Earth's atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taeda L.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.
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Affiliation(s)
- Lilian P. Matallana-Ramirez
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Georgina M. Sanchez
- Center for Geospatial Analytics, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Kitt G. Payn
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
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Li Y, Guo Q, Liu P, Huang J, Zhang S, Yang G, Wu C, Zheng C, Yan K. Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:641-655. [PMID: 33421141 DOI: 10.1111/nph.17175] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/23/2020] [Indexed: 05/23/2023]
Abstract
Alternative splicing (AS) is emerging as a critical co-transcriptional regulation for plants in response to environmental stresses. Although multiple splicing factors have been linked to the salt-sensitive signaling network, the molecular mechanism remains unclear. We discovered that a conserved serine/arginine-rich (SR)-like protein, SR45a, as a component of the spliceosome, was involved in post-transcriptional regulation of salinity tolerance in Arabidopsis thaliana. Furthermore, SR45a was required for the AS and messenger RNA (mRNA) maturation of several salt-tolerance genes. Two alternatively spliced variants of SR45a were induced by salt stress, full-length SR45a-1a and the truncated isoform SR45a-1b, respectively. Lines with overexpression of SR45a-1a and SR45a-1b exhibited hypersensitive to salt stress. Our data indicated that SR45a directly interacted with the cap-binding complex (CBC) subunit cap-binding protein 20 (CBP20) which mediated salt-stress responses. Instead of binding to other spliceosome components, SR45a-1b promoted the association of SR45a-1a with CBP20, therefore mediating salt-stress signal transduction pathways. Additionally, the mutations in SR45a and CBP20 led to different salt-stress phenotypes. Together, these results provide the evidence that SR45a-CBP20 acts as a regulatory complex to regulate the plant response to salt stress, through a regulatory mechanism to fine-tune the splicing factors, especially in stressful conditions.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Qianhuan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
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63
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Liu S, Qin F. Genetic dissection of maize drought tolerance for trait improvement. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:8. [PMID: 37309476 PMCID: PMC10236036 DOI: 10.1007/s11032-020-01194-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/27/2020] [Indexed: 06/13/2023]
Abstract
Maize is one of the most important crops, but its production is threatened by drought stress worldwide. Thus, increased drought tolerance has been a major goal of maize breeding. Conventional breeding strategies have led to significantly increase of maize yields; however, these strategies often fail to meet the need for drought stress tolerance enhancement. Here, we focus on progress related to the genetic dissection of drought tolerance in maize at different developmental stages achieved through linkage mapping and association mapping. Moreover, recent molecular breeding systems, including transgenic, genome-wide marker-assisted selection, and genome editing technologies, have provided a more direct, efficient, and accurate approach for trait improvement. We also provide perspectives on future directions regarding multi-omics studies and maize improvement. Overall, the application of acquired knowledge will facilitate maize breeding to meet the challenges.
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Affiliation(s)
- Shengxue Liu
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Feng Qin
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
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Song L, Pan Z, Chen L, Dai Y, Wan J, Ye H, Nguyen HT, Zhang G, Chen H. Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions. Genes (Basel) 2020; 11:E1520. [PMID: 33352659 PMCID: PMC7765832 DOI: 10.3390/genes11121520] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3' splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants.
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Affiliation(s)
- Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Zhenzhi Pan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Lin Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Yi Dai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; (Z.P.); (L.C.); (Y.D.)
| | - Jinrong Wan
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Heng Ye
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (J.W.); (H.Y.); (H.T.N.)
| | - Guozheng Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China;
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
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66
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Fang S, Hou X, Qiu K, He R, Feng X, Liang X. The occurrence and function of alternative splicing in fungi. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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67
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Wang R, Yin P, Ruixia Y, Liu X, Luo L, Xu J. Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves. PLoS One 2020; 15:e0241914. [PMID: 33206683 PMCID: PMC7673502 DOI: 10.1371/journal.pone.0241914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.
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Affiliation(s)
- Ruixue Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Peng Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Yang Ruixia
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Xiao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Lie Luo
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jichen Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- * E-mail:
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68
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Chen MX, Zhang KL, Zhang M, Das D, Fang YM, Dai L, Zhang J, Zhu FY. Alternative splicing and its regulatory role in woody plants. TREE PHYSIOLOGY 2020; 40:1475-1486. [PMID: 32589747 DOI: 10.1093/treephys/tpaa076] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.
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Affiliation(s)
- Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Dai
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation. G3-GENES GENOMES GENETICS 2020; 10:3709-3717. [PMID: 32763954 PMCID: PMC7534434 DOI: 10.1534/g3.120.400794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.
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Yan Z, Shen Z, Li Z, Chao Q, Kong L, Gao ZF, Li QW, Zheng HY, Zhao CF, Lu CM, Wang YW, Wang BC. Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings. PLANTA 2020; 252:60. [PMID: 32964359 DOI: 10.1007/s00425-020-03464-5] [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: 05/22/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Zhe Li
- Precision Scientific (Beijing) Co., Ltd., Beijing, 100085, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Qing-Wei Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Yan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ, 08855, USA
| | - Cai-Feng Zhao
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ, 08855, USA
| | - Cong-Ming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Ying-Wei Wang
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China.
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71
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Pootakham W, Nawae W, Naktang C, Sonthirod C, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Somta P, Laosatit K, Tangphatsornruang S. A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 2020; 21:238-250. [PMID: 32794377 DOI: 10.1111/1755-0998.13243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
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Zhu Z, Chen H, Xie K, Liu C, Li L, Liu L, Han X, Jiao C, Wan Z, Sha A. Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean ( Vigna angularis L.) by PacBio SMRT and Illumina Sequencing. Front Genet 2020; 11:996. [PMID: 33110419 PMCID: PMC7489039 DOI: 10.3389/fgene.2020.00996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 08/05/2020] [Indexed: 11/13/2022] Open
Abstract
The full-length single-molecular sequencing and short reads Illumina sequencing were combined to generate the transcripts of adzuki bean with high-quality. A total of 17,636 loci and 60,454 transcripts were detected in this study. To characterize the drought-responsive genes during seed germination in adzuki bean, two varieties, i.e., tolerant and sensitive to drought stress, were selected to conduct analysis of alternative splicing dynamics (AS) and differentially expressed genes (DEGs) by combining the newly assembled draft genome and public adzuki bean reference genome. AS analysis indicated that both the two varieties underwent a little more AS events under control conditions than under drought stress. Among the AS events, IR (intron retention) predominately accounted for 34.3%, whereas AD (alternative donor site) was the least frequent with 15.8%. Meanwhile, 562 long non-coding RNAs, 409 fusion genes and 1208 transcription factors were identified. Moreover, a total of 5,337 DEGs were identified in comparison of the two varieties with drought or control treatments. Notably, 82 DEGs were discovered in the two varieties under drought stress, which might be the candidate in regulation of seed germination to answer for different drought tolerance. The DEGs encoded proteins involved in primary or second metabolism, plant hormone signal transduction, transcript or translation processes, ubiquitin proteasome system, transcription factor, transporters, and so on. The results facilitate to increase the knowledge about the mechanism of drought tolerance during crop seed germination, and provide reference for the breeding of drought-tolerant adzuki bean.
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Affiliation(s)
- Zhenzhen Zhu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou, China
| | - Hongwei Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Ke Xie
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing, China
| | - Changyan Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Li Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Liangjun Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Xuesong Han
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Chunhai Jiao
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Zhenghuang Wan
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Aihua Sha
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou, China
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Pootakham W, Sonthirod C, Naktang C, Nawae W, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Sheedy JR, Buaboocha J, Mekiyanon S, Tangphatsornruang S. De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements. Mol Ecol Resour 2020; 21:212-225. [PMID: 32841550 DOI: 10.1111/1755-0998.13240] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023]
Abstract
Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold N50 of 786,130 and 578,616 bases for L. acutangula and L. cylindrica, respectively. We also applied long-range Chicago and HiC techniques to obtain the first chromosome-scale whole-genome assembly of L. acutangula. The final assembly contained 13 pseudomolecules, corresponding to the haploid chromosome number in Luffa spp. (1n = 13, 2n = 26). The sizes of the assembled Luffa genomes are approximately twice as large as the genome assemblies of related Cucurbitaceae. A large proportion of L. acutangula (62.17%; 456.69 Mb) and L. cylindrica (56.78%; 391.65 Mb) genome assemblies contained repetitive elements. Phylogenetic analyses revealed that the substantial accumulation of transposable elements likely contributed to the expansion of the Luffa genomes. We also investigated alternative splicing events in Luffa using full-length transcript sequences obtained from PacBio Isoform Sequencing (Iso-seq). While the predominant form of alternative splicing in most plant species examined was intron retention, alternative 3' acceptor site selection appeared to be a major event observed in Luffa. High-quality genome assemblies for L. acutangula and L. cylindrica reported here provide valuable resources for Luffa breeding and future genetics and comparative genomics studies in Cucurbitaceae.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - John R Sheedy
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
| | | | - Supat Mekiyanon
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
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Huang L, Zhang L, Zeng R, Wang X, Zhang H, Wang L, Liu S, Wang X, Chen T. Brassinosteroid Priming Improves Peanut Drought Tolerance via Eliminating Inhibition on Genes in Photosynthesis and Hormone Signaling. Genes (Basel) 2020; 11:genes11080919. [PMID: 32796553 PMCID: PMC7465412 DOI: 10.3390/genes11080919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 01/11/2023] Open
Abstract
Drought negatively affects the growth and yield of terrestrial crops. Seed priming, pre-exposing seed to a compound, could induce improved tolerance and adaptation to stress in germinated plants. To understand the effects and regulatory mechanism of seed priming with brassinosteroid (BR) on peanut plants, we treated seeds with five BR concentrations and examined dozens of physiological and biochemical features, and transcriptomic changes in leaves under well-watered and drought conditions. We found optimal 0.15 ppm BR priming could reduce inhibitions from drought and increase the yield of peanut, and priming effects are dependent on stage of plant development and duration of drought. BR priming induced fewer differentially expressed genes (DEGs) than no BR priming under well-watered condition. Drought with BR priming reduced the number of DEGs than drought only. These DEGs were enriched in varied gene ontologies and metabolism pathways. Downregulation of DEGs involved in both light perceiving and photosynthesis in leaves is consistent with low parameters of photosynthesis. Optimal BR priming partially rescued the levels of growth promoting auxin and gibberellin which were largely reduced by drought, and increased levels of defense associated abscisic acid and salicylic acid after long-term drought. BR priming induced many DEGs which function as kinase or transcription factor for signal cascade under drought. We proposed BR priming-induced regulatory responses will be memorized and recalled for fast adaptation in later drought stress. These results provide physiological and regulatory bases of effects of seed priming with BR, which can help to guide the framing improvement under drought stress.
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Affiliation(s)
- Luping Huang
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Lei Zhang
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Ruier Zeng
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Xinyue Wang
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Huajian Zhang
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Leidi Wang
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Shiyuan Liu
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Correspondence: (X.W.); (T.C.)
| | - Tingting Chen
- Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.H.); (L.Z.); (R.Z.); (X.W.); (H.Z.); (L.W.); (S.L.)
- Correspondence: (X.W.); (T.C.)
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75
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Niyikiza D, Piya S, Routray P, Miao L, Kim WS, Burch-Smith T, Gill T, Sams C, Arelli PR, Pantalone V, Krishnan HB, Hewezi T. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1744-1766. [PMID: 32491251 DOI: 10.1111/tpj.14861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/19/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.
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Affiliation(s)
- Daniel Niyikiza
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Pratyush Routray
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Long Miao
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won-Seok Kim
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Tom Gill
- Smith Center for International Sustainable Agriculture, University of Tennessee, Knoxville, TN, 37996, USA
| | - Carl Sams
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
- Plant Genetics Research, USDA-Agricultural Research Service, Columbia, MI, 65211, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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76
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Feng G, Yoo M, Davenport R, Boatwright JL, Koh J, Chen S, Barbazuk WB. Jasmonate induced alternative splicing responses in Arabidopsis. PLANT DIRECT 2020; 4:e00245. [PMID: 32875268 PMCID: PMC7450174 DOI: 10.1002/pld3.245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/04/2020] [Accepted: 06/24/2020] [Indexed: 05/14/2023]
Abstract
Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA- and RNA-binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty-one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators. SIGNIFICANCE STATEMENT By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA-mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.
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Affiliation(s)
- Guanqiao Feng
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
| | - Mi‐Jeong Yoo
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Ruth Davenport
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | | | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
| | - Sixue Chen
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - W. Brad Barbazuk
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
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Qiu Z, Chen S, Qi Y, Liu C, Zhai J, Xie S, Ma C. Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS. Brief Bioinform 2020; 22:5877690. [PMID: 32728687 DOI: 10.1093/bib/bbaa137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/25/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal or other dimensions. TS has been associated with human diseases, plant development and stress responses. Its investigation is often hampered by a lack of suitable tools allowing comprehensive and flexible TS analysis for high-throughput RNA sequencing (RNA-Seq) data. Here, we present deepTS, a user-friendly web-based implementation that enables a fully interactive, multifunctional identification, visualization and analysis of TS events for large-scale RNA-Seq datasets from pairwise, temporal and population experiments. deepTS offers rich functionality to streamline RNA-Seq-based TS analysis for both model and non-model organisms and for those with or without reference transcriptome. The presented case studies highlight the capabilities of deepTS and demonstrate its potential for the transcriptome-wide TS analysis of pairwise, temporal and population RNA-Seq data. We believe deepTS will help research groups, regardless of their informatics expertise, perform accessible, reproducible and collaborative TS analyses of large-scale RNA-Seq data.
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Affiliation(s)
| | | | | | | | | | | | - Chuang Ma
- Bioinformatics Laboratory at Northwest A&F University
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78
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Wang Z, Ma W, Zhu T, Lu N, Ouyang F, Wang N, Yang G, Kong L, Qu G, Zhang S, Wang J. Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey. BMC Genomics 2020; 21:508. [PMID: 32698759 PMCID: PMC7376858 DOI: 10.1186/s12864-020-06918-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perennial woody plants. "Bairihua" is a type of C. bungei that can undergo floral transition in the first planting year. RESULTS Here, we combined short-read next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to provide a more complete view of transcriptome regulation during floral transition in C. bungei. The circadian rhythm-plant pathway may be the critical pathway during floral transition in early flowering (EF) C. bungei, according to horizontal and vertical analysis in EF and normal flowering (NF) C. bungei. SBP and MIKC-MADS-box were seemingly involved in EF during floral transition. A total of 61 hub genes were associated with floral transition in the MEturquoise model with Weighted Gene Co-expression Network Analysis (WGCNA). The results reveal that ten hub genes had a close connection with the GASA homologue gene (Cbu.gene.18280), and the ten co-expressed genes belong to five flowering-related pathways. Furthermore, our study provides new insights into the complexity and regulation of alternative splicing (AS). The ratio or number of isoforms of some floral transition-related genes is different in different periods or in different sub-genomes. CONCLUSIONS Our results will be a useful reference for the study of floral transition in other perennial woody plants. Further molecular investigations are needed to verify our sequencing data.
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Affiliation(s)
- Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Fangqun Ouyang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Lisheng Kong
- Department of Biology Centre for Forest Biology, University of Victoria, Victoria, BC 11 Canada
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 PR China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 PR China
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Barreto P, Couñago RM, Arruda P. Mitochondrial uncoupling protein-dependent signaling in plant bioenergetics and stress response. Mitochondrion 2020; 53:109-120. [DOI: 10.1016/j.mito.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/06/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
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80
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Zhang Y, Rahmani RS, Yang X, Chen J, Shi T. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC Genomics 2020; 21:429. [PMID: 32586276 PMCID: PMC7315500 DOI: 10.1186/s12864-020-06853-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 01/29/2023] Open
Abstract
Background Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Results Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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81
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Yang H, Xu D, Zhuo Z, Hu J, Lu B. SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PeerJ 2020; 8:e9133. [PMID: 32509454 PMCID: PMC7246026 DOI: 10.7717/peerj.9133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.
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Affiliation(s)
- Hongjun Yang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Danping Xu
- Sichuan Provincial Key Laboratory of Agricultural Products Processing and Preservative, College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, China
| | - Zhihang Zhuo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China.,Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiameng Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Baoqian Lu
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Noble JD, Balmant KM, Dervinis C, de los Campos G, Resende MFR, Kirst M, Barbazuk WB. The Genetic Regulation of Alternative Splicing in Populus deltoides. FRONTIERS IN PLANT SCIENCE 2020; 11:590. [PMID: 32582229 PMCID: PMC7291814 DOI: 10.3389/fpls.2020.00590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Alternative splicing (AS) is a mechanism of regulation of the proteome via enabling the production of multiple mRNAs from a single gene. To date, the dynamics of AS and its effects on the protein sequences of individuals in a large and genetically unrelated population of trees have not been investigated. Here we describe the diversity of AS events within a previously genotyped population of 268 individuals of Populus deltoides and their putative downstream functional effects. Using a robust bioinformatics pipeline, the AS events and resulting transcript isoforms were discovered and quantified for each individual in the population. Analysis of the AS revealed that, as expected, most AS isoforms are conserved. However, we also identified a substantial collection of new, unannotated splice junctions and transcript isoforms. Heritability estimates for the expression of transcript isoforms showed that approximately half of the isoforms are heritable. The genetic regulators of these AS isoforms and splice junction usage were then identified using a genome-wide association analysis. The expression of AS isoforms was predominately cis regulated while splice junction usage was generally regulated in trans. Additionally, we identified 696 genes encoding alternatively spliced isoforms that changed putative protein domains relative to the longest protein coding isoform of the gene, and 859 genes exhibiting this same phenomenon relative to the most highly expressed isoform. Finally, we found that 748 genes gained or lost micro-RNA binding sites relative to the longest protein coding isoform of a given gene, while 940 gained or lost micro-RNA binding sites relative to the most highly expressed isoform. These results indicate that a significant fraction of AS events are genetically regulated and that this isoform usage can result in protein domain architecture changes.
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Affiliation(s)
- Jerald D. Noble
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Kelly M. Balmant
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Gustavo de los Campos
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
| | - Márcio F. R. Resende
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Matias Kirst
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - William Brad Barbazuk
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
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83
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Dwivedi SL, Stoddard FL, Ortiz R. Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110365. [PMID: 32534611 DOI: 10.1016/j.plantsci.2019.110365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/15/2019] [Accepted: 12/01/2019] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.
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Affiliation(s)
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, SE 23053, Alnarp, Sweden.
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84
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Lee WC, Hou BH, Hou CY, Tsao SM, Kao P, Chen HM. Widespread Exon Junction Complex Footprints in the RNA Degradome Mark mRNA Degradation before Steady State Translation. THE PLANT CELL 2020; 32:904-922. [PMID: 31988264 PMCID: PMC7145476 DOI: 10.1105/tpc.19.00666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/02/2019] [Accepted: 01/24/2020] [Indexed: 05/13/2023]
Abstract
Exon junction complexes (EJCs) are deposited on mRNAs during splicing and displaced by ribosomes during the pioneer round of translation. Nonsense-mediated mRNA decay (NMD) degrades EJC-bound mRNA, but the lack of suitable methodology has prevented the identification of other degradation pathways. Here, we show that the RNA degradomes of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), worm (Caenorhabditis elegans), and human (Homo sapiens) cells exhibit an enrichment of 5' monophosphate (5'P) ends of degradation intermediates that map to the canonical EJC region. Inhibition of 5' to 3' exoribonuclease activity and overexpression of an EJC disassembly factor in Arabidopsis reduced the accumulation of these 5'P ends, supporting the notion that they are in vivo EJC footprints. Hundreds of Arabidopsis NMD targets possess evident EJC footprints, validating their degradation during the pioneer round of translation. In addition to premature termination codons, plant microRNAs can also direct the degradation of EJC-bound mRNAs. However, the production of EJC footprints from NMD but not microRNA targets requires the NMD factor SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN7. Together, our results demonstrating in vivo EJC footprinting in Arabidopsis unravel the composition of the RNA degradome and provide a new avenue for studying NMD and other mechanisms targeting EJC-bound mRNAs for degradation before steady state translation.
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Affiliation(s)
- Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Yu Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Ming Tsao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ping Kao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
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85
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Sun Y, Zhang Q, Liu B, Lin K, Zhang Z, Pang E. CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. BMC PLANT BIOLOGY 2020; 20:119. [PMID: 32183712 PMCID: PMC7079458 DOI: 10.1186/s12870-020-2312-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation. DESCRIPTION To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene. CONCLUSION We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php.
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Affiliation(s)
- Ying Sun
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, No 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Bing Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and 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 and 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
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and 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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86
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Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos. Nat Commun 2020; 11:1366. [PMID: 32170064 PMCID: PMC7070050 DOI: 10.1038/s41467-020-15189-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells. However, the genome-wide transcriptional activities that guide divergence of apical and basal cell development remain unknown. Here, we present a comprehensive transcriptome analysis of apical and basal cell lineages, uncovering distinct molecular pathways during cell lineage specification. Selective deletion of inherited transcripts and specific de novo transcription contribute to the establishment of cell lineage-specific pathways for cell fate specification. Embryo-related pathways have been specifically activated in apical cell lineage since 1-cell embryo stage, but quick transcriptome remodeling toward suspensor-specific pathways are found in basal cell lineage. Furthermore, long noncoding RNAs and alternative splicing isoforms may be involved in cell lineage specification. This work also provides a valuable lineage-specific transcriptome resource to elucidate the molecular pathways for divergence of apical and basal cell lineages at genome-wide scale. Asymmetric division of the Arabidopsis zygote produces apical and basal cells that mainly develop into embryo and suspensor, respectively. Here, Zhou et al. show that de novo transcription and selective RNA turnover establish distinct apical and basal transcriptomes as early as the 1-cell stage of embryo development.
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87
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Dubois M, Inzé D. Plant growth under suboptimal water conditions: early responses and methods to study them. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1706-1722. [PMID: 31967643 DOI: 10.1093/jxb/eraa037] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 05/03/2023]
Abstract
Drought stress forms a major environmental constraint during the life cycle of plants, often decreasing plant yield and in extreme cases threatening survival. The molecular and physiological responses induced by drought have been the topic of extensive research during the past decades. Because soil-based approaches to studying drought responses are often challenging due to low throughput and insufficient control of the conditions, osmotic stress assays in plates were developed to mimic drought. Addition of compounds such as polyethylene glycol, mannitol, sorbitol, or NaCl to controlled growth media has become increasingly popular since it offers the advantage of accurate control of stress level and onset. These osmotic stress assays enabled the discovery of very early stress responses, occurring within seconds or minutes following osmotic stress exposure. In this review, we construct a detailed timeline of early responses to osmotic stress, with a focus on how they initiate plant growth arrest. We further discuss the specific responses triggered by different types and severities of osmotic stress. Finally, we compare short-term plant responses under osmotic stress versus in-soil drought and discuss the advantages, disadvantages, and future of these plate-based proxies for drought.
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Affiliation(s)
- Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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88
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Zhong R, Wang Y, Gai R, Xi D, Mao C, Ming F. Rice SnRK protein kinase OsSAPK8 acts as a positive regulator in abiotic stress responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110373. [PMID: 32005379 DOI: 10.1016/j.plantsci.2019.110373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/04/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
SnRK2 (sucrose non-fermenting 1-related protein kinases 2) protein kinase family involves in several abiotic stress response in plants. Although the regulatory mechanism of SnRK2 have been well demonstrated in Arabidopsis thaliana, their functions in rice are still largely unknown. Here, we report a SnRK2 family gene, OsSAPK8, can be strongly induced by abiotic stresses, including low-temperature, drought and high salt stress. The ossapk8 mutants showed lower tolerance to low-temperature, high salinity and drought stresses at the vegetative stages. Moreover, the expressions of marker genes for those abiotic stresses, e.g. OsDREB1, OsDREB2, OsNCED and OsRAB21, were downregulated in the ossapk8 mutants. We further confirmed that the yield was reduced in ossapk8 mutant lines compared with the wild type. Our results provide evidence for OsSAPK8 acting as a positive regulator in cold, drought, and salt stress responses.
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Affiliation(s)
- Ruiling Zhong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Science, Fudan University, Shanghai 200433, China
| | - Yuxia Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Science, Fudan University, Shanghai 200433, China; Institute of Biothermal Science and Technology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ruonan Gai
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Dandan Xi
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Science, Fudan University, Shanghai 200433, China
| | - Chanjuan Mao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Science, Fudan University, Shanghai 200433, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Science, Fudan University, Shanghai 200433, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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89
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Ding Y, Wang Y, Qiu C, Qian W, Xie H, Ding Z. Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses. PeerJ 2020; 8:e8258. [PMID: 32030318 PMCID: PMC6995271 DOI: 10.7717/peerj.8258] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022] Open
Abstract
Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for 48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance.
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Affiliation(s)
- Yiqian Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Hui Xie
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
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90
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Li Y, Mi X, Zhao S, Zhu J, Guo R, Xia X, Liu L, Liu S, Wei C. Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant. BMC Genomics 2020; 21:65. [PMID: 31959105 PMCID: PMC6971990 DOI: 10.1186/s12864-020-6491-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/13/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis). RESULTS In this study, the AS transcriptional landscape was characterized in the tea plant genome using high-throughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents. CONCLUSION Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.
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Affiliation(s)
- Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Lu Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
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91
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Li Z, Huang T, Tang M, Cheng B, Peng Y, Zhang X. iTRAQ-based proteomics reveals key role of γ-aminobutyric acid (GABA) in regulating drought tolerance in perennial creeping bentgrass (Agrostis stolonifera). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:216-226. [PMID: 31707249 DOI: 10.1016/j.plaphy.2019.10.018] [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: 07/23/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 05/22/2023]
Abstract
γ-Aminobutyric acid (GABA), a non-proteinaceous amino acid, modulates plant growth and stress tolerance. However, the potential role of GABA in regulating key metabolic pathways and stress-defensive proteins against drought in plants has never been explored. Creeping bentgrass (Agrostis stolonifera) plants were pretreated with or without GABA and then subjected to water stress for 8 days in controlled growth chambers (23/19 °C, day/night). Physiological analysis showed that elevated endogenous GABA level via exogenous GABA application significantly mitigated water stress damage to creeping bentgrass, as manifested by increased leaf relative water content, water use efficiency, osmotic adjustment (OA), photochemical efficiency (Fv/Fm), net photosynthetic rate, and reduced oxidative damage. iTRAQ-based proteomics found that enhanced chaperones accumulation, carbohydrates, amino acids, and energy metabolism played important roles in protein protection, OA, energy maintenance, and metabolic balance, which is important adaptive response to drought stress in creeping bentgrass. The GABA further promoted energy production and conversion, antioxidant defense, and DHN3 accumulation that were essential for energy requirement, ROS-scavenging, and the prevention of cell dehydration in leaf during drought stress. In addition, GABA-treated plants maintained significantly higher abundance of dicarboxylate transporter 2.1, ATP-dependent zinc metalloprotease, receptor-like protein kinase HERK1, o-acyltransferase WSD1, omega-6 fatty acid desaturase, and two-component response regulator ORR21 than untreated plants under drought stress. The result provides new evidences that GABA-induced drought tolerance is possibly involved in the improvement of nitrogen recycling, protection of photosystem II, mitigation of drought-depressed cell elongation, wax biosynthesis, fatty acid desaturase, and delaying leaf senescence in creeping bentgrass.
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Affiliation(s)
- Zhou Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Huang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingyan Tang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binzhen Cheng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Peng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Li MH, Liu DK, Zhang GQ, Deng H, Tu XD, Wang Y, Lan SR, Liu ZJ. A perspective on crassulacean acid metabolism photosynthesis evolution of orchids on different continents: Dendrobium as a case study. JOURNAL OF EXPERIMENTAL BOTANY 2019; 71:422-434. [PMID: 31625570 DOI: 10.1093/jxb/erz444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/24/2019] [Indexed: 05/24/2023]
Abstract
Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium, which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than -20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents.
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Affiliation(s)
- Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Hua Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiong-De Tu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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93
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Wang L, Chen M, Zhu F, Fan T, Zhang J, Lo C. Alternative splicing is a Sorghum bicolor defense response to fungal infection. PLANTA 2019; 251:14. [PMID: 31776670 DOI: 10.1007/s00425-019-03309-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/29/2019] [Indexed: 05/24/2023]
Abstract
This study provides new insights that alternative splicing participates with transcriptional control in defense responses to Colletotrichum sublineola in sorghum In eukaryotic organisms, alternative splicing (AS) is an important post-transcriptional mechanism to generate multiple transcript isoforms from a single gene. Protein variants translated from splicing isoforms may have altered molecular characteristics in signal transduction and metabolic activities. However, which transcript isoforms will be translated into proteins and the biological functions of the resulting proteoforms are yet to be identified. Sorghum is one of the five major cereal crops, but its production is severely affected by fungal diseases. For example, sorghum anthracnose caused by Colletotrichum sublineola greatly reduces grain yield and biomass production. In this study, next-generation sequencing technology was used to analyze C. sublineola-inoculated sorghum seedlings compared with mock-inoculated control. It was identified that AS regulation may be as important as traditional transcriptional control during defense responses to fungal infection. Moreover, several genes involved in flavonoid and phenylpropanoid biosynthetic pathways were found to undergo multiple AS modifications. Further analysis demonstrated that non-conventional targets of both 5'- and 3'-splice sites were alternatively used in response to C. sublineola infection. Splicing factors were also affected at both transcriptional and post-transcriptional levels. As the first transcriptome report on C. sublineola infected sorghum, our work also suggested that AS plays crucial functions in defense responses to fungal invasion.
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Affiliation(s)
- Lanxiang Wang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Moxian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fuyuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Tao Fan
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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94
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Zhang H, Mao R, Wang Y, Zhang L, Wang C, Lv S, Liu X, Wang Y, Ji W. Transcriptome-wide alternative splicing modulation during plant-pathogen interactions in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110160. [PMID: 31521219 DOI: 10.1016/j.plantsci.2019.05.023] [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: 12/29/2018] [Revised: 03/11/2019] [Accepted: 05/29/2019] [Indexed: 05/07/2023]
Abstract
Alternative splicing (AS) enhances the diversities of both transcripts and proteins in eukaryotes, which contribute to stress adaptation. To catalog wheat (Triticum aestivum L.) AS genes, we characterized 45 RNA-seq libraries from wheat seedlings infected by powdery mildew, Blumeria graminis f. sp. tritici (Bgt) or stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst). We discovered that 11.2% and 10.4% of the multiexon genes had AS transcripts during Bgt and Pst infections, respectively. In response to fungal infection, wheat modulated AS not only in disease resistance proteins, but also in splicing related factors. Apart from the stress induced or activated splicing variants by pathogen, the differential expression profiles were fold increased through changing the ratio of full spliced transcripts versus intron retention (IR) transcripts. Comparing AS transcripts produced by the same gene in Bgt with Pst stress, the spliced terminal exons and the stranded introns are independent and different. This demonstrated that differential induction of specific splice variants were activated against two fungal pathogens. The specific induced AS genes in the Pst-resistant plants were enriched in improving the membrane permeability and protein modification ability, whereas gene expression involved in protein translation and transport were strengthened in Pst-susceptible plants.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Rui Mao
- College of Information Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Shikai Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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95
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Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites. Proc Natl Acad Sci U S A 2019; 116:22376-22385. [PMID: 31611386 PMCID: PMC6825267 DOI: 10.1073/pnas.1906244116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Highly ABA-Induced 1 (HAI1) protein phosphatase is a central component of drought-related signaling. A screen for HAI1-interacting proteins identified HAI1-Interactor 1 (HIN1), a nuclear protein of unknown function which could be dephosphorylated by HAI1 in vitro. HIN1 colocalization and interaction with serine-arginine rich (SR) splicing factors and appearance of nuclear speckle-localized HIN1 during low water potential (ψw) stress suggested a pre-mRNA splicing-related function. RNA sequencing of Arabidopsis Col-0 wild type identified more than 500 introns where moderate severity low ψw altered intron retention (IR) frequency. Surprisingly, nearly 90% of these had increased splicing efficiency (decreased IR) during stress. For one-third of these introns, ectopic HIN1 expression (35S:HIN1) in unstressed plants mimicked the increased splicing efficiency seen in stress-treated wild type. HIN1 bound to a GAA-repeat, Exonic Splicing Enhancer-like RNA motif enriched in flanking sequence around HIN1-regulated introns. Genes with stress and HIN1-affected splicing efficiency were enriched for abiotic stress and signaling-related functions. The 35S:HIN1 plants had enhanced growth maintenance during low ψw, while hin1 mutants had reduced growth, further indicating the role of HIN1 in drought response. HIN1 is annotated as an MYB/SANT domain protein but has limited homology to other MYB/SANT proteins and is not related to known yeast or metazoan RNA-binding proteins or splicing regulators. Together these data identify HIN1 as a plant-specific RNA-binding protein, show a specific effect of drought acclimation to promote splicing efficiency of IR-prone introns, and also discover HAI1-HIN1 interaction and dephosphorylation that connects stress signaling to splicing regulation.
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96
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Ji S, Liu Z, Liu B, Wang Y. Comparative analysis of biocontrol agent Trichoderma asperellum ACCC30536 transcriptome during its interaction with Populus davidiana × P. alba var. pyramidalis. Microbiol Res 2019; 227:126294. [PMID: 31421718 DOI: 10.1016/j.micres.2019.126294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
After exposure to with Populus davidiana × P. alba var. pyramidalis, the expression of genes in Trichoderma asperellum were compared in four transcriptomes. The top 20 high expression genes included six heat shock proteins and three hydrophobins, indicating that Trichoderma can rapidly adapt to environment stresses and elicit a plant defense response. The genes, involved in the interaction between Trichoderma and plant, showed an increasing expression level, for example sugar transporters, EPL1s, endoxylanases, pectin lyases, and nitrilases. Interestingly, sugar transporters also showed high expression when T. asperellum was cultured on medium lacking a carbon substrate, which would contribute to T. asperellum's survival and domination in ecological niche competition. And the genes related to mycoparasitism were expressed abundantly following T. asperellum's interaction with PdPap, indicating the PdPap induction could enhance the mycoparasitic ability of T. asperellum. Twelve chitinases and five glucanases showed higher expression in transcriptome Cs, indicating that T. asperellum secretes both types of enzyme before interacting with pathogens, allowing T. asperellum to implement mycoparasitism and obtain more energy. Many novel transcripts were obtained in each transcriptome, which may play important roles in the biocontrol process of T. asperellum. Interestingly, T. asperellum undergo constitutive alternative splicing in the biocontrol process: Seven biocontrol genes were alternative spliced via intron retention. qRT-PCR analysis proved that intron retention is negatively associated with the expression of chitinase, oligopeptide transporters, and beta-lactamase. However, the percentage of MAPK intron retention was quite low, suggesting that intron retention has little effect on the function of MAPK.
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Affiliation(s)
- Shida Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Zhihua Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Bin Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040, Harbin, China.
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97
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Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation. Int J Mol Sci 2019; 20:ijms20123101. [PMID: 31242611 PMCID: PMC6627786 DOI: 10.3390/ijms20123101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 11/24/2022] Open
Abstract
Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginellamoellendorffii. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.
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98
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Bedre R, Irigoyen S, Schaker PDC, Monteiro-Vitorello CB, Da Silva JA, Mandadi KK. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Sci Rep 2019; 9:8876. [PMID: 31222001 PMCID: PMC6586842 DOI: 10.1038/s41598-019-45184-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
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Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
| | - Patricia D C Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
- Universidade Tecnológica Federal do Paraná, Toledo, Paraná, Brazil
| | - Claudia B Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz," Piracicaba, São Paulo, Brazil
| | - Jorge A Da Silva
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University, Weslaco, TX, USA.
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, USA.
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99
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Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish ( Danio rerio). G3-GENES GENOMES GENETICS 2019; 9:1831-1838. [PMID: 30872328 PMCID: PMC6553537 DOI: 10.1534/g3.119.200997] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform first. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately 62.27% of the 12,782 genes have been alternatively spliced. GO and KEGG annotations revealed that the unfertilized eggs primarily stored genes that participate in RNA processing and nuclear protein complex composition. According to this PacBio data that aligned with the genome, 3,970 fusion genes, 819 ncRNAs, and 84 new transcripts were predicted. Illumina RNA-seq and RT-qPCR detection found that the expression of two new transcripts, PB.5289.1 and PB.10209.1, were significantly up-regulated at the 2-cell stage and down-regulated rapidly thereafter, suggesting their involvement in minor ZGA during early embryonic development. This study indicated that the unfertilized eggs of zebrafish may have retained genes directly related to cell division and development to initiate the subsequent development in a limited space and time. On the other hand, NTRs or new transcriptome regions in the genome were discovered, which provided new clues regarding ZGA of MZT during early embryonic development in fish.
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100
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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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