Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing
Genetic male sterility (GMS) facilitates hybrid seed production in crops including cotton ( Gossypium hirsutum ). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and tr...
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description | Genetic male sterility (GMS) facilitates hybrid seed production in crops including cotton (
Gossypium hirsutum
). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and transcriptome sequencing were performed to analyze miRNAs and their target genes during anther development in a GMS mutant (‘Dong A’) and its fertile wildtype (WT). A total of 80 known and 220 novel miRNAs were identified, 71 of which showed differential expressions during anther development. A further degradome sequencing revealed a total of 117 candidate target genes cleaved by 16 known and 36 novel miRNAs. Based on RNA-seq, 24, 11, and 21 predicted target genes showed expression correlations with the corresponding miRNAs at the meiosis, tetrad and uninucleate stages, respectively. In addition, a large number of differentially expressed genes were identified, most of which were involved in sucrose and starch metabolism, carbohydrate metabolism, and plant hormone signal transduction based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The results of our study provide valuable information for further functional investigations of the important miRNAs and target genes involved in genetic male sterility and advance our understanding of miRNA regulatory functions during cotton anther development. |
doi_str_mv | 10.1007/s00438-020-01656-y |
format | Article |
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Gossypium hirsutum
). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and transcriptome sequencing were performed to analyze miRNAs and their target genes during anther development in a GMS mutant (‘Dong A’) and its fertile wildtype (WT). A total of 80 known and 220 novel miRNAs were identified, 71 of which showed differential expressions during anther development. A further degradome sequencing revealed a total of 117 candidate target genes cleaved by 16 known and 36 novel miRNAs. Based on RNA-seq, 24, 11, and 21 predicted target genes showed expression correlations with the corresponding miRNAs at the meiosis, tetrad and uninucleate stages, respectively. In addition, a large number of differentially expressed genes were identified, most of which were involved in sucrose and starch metabolism, carbohydrate metabolism, and plant hormone signal transduction based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The results of our study provide valuable information for further functional investigations of the important miRNAs and target genes involved in genetic male sterility and advance our understanding of miRNA regulatory functions during cotton anther development.</description><identifier>ISSN: 1617-4615</identifier><identifier>EISSN: 1617-4623</identifier><identifier>DOI: 10.1007/s00438-020-01656-y</identifier><identifier>PMID: 32172356</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Biochemistry ; Biomedical and Life Sciences ; Carbohydrate metabolism ; Cotton ; Flowers - genetics ; Flowers - growth & development ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Genomes ; Gossypium - genetics ; Gossypium - growth & development ; Gossypium hirsutum ; High-Throughput Nucleotide Sequencing ; Human Genetics ; Life Sciences ; Male sterility ; Meiosis ; Metabolism ; Microbial Genetics and Genomics ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Molecular modelling ; Mutants ; Mutation ; Original ; Original Article ; Plant Genetics and Genomics ; Plant Infertility - genetics ; Plant Proteins - genetics ; Plants, Genetically Modified - genetics ; Plants, Genetically Modified - growth & development ; Signal transduction ; Starch ; Sucrose ; Transcriptome</subject><ispartof>Molecular genetics and genomics : MGG, 2020-05, Vol.295 (3), p.645-660</ispartof><rights>The Author(s) 2020</rights><rights>The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-62a642b08238f9ca642586770b94f0f51a7f35bc193be2a173b900c4822550e13</citedby><cites>FETCH-LOGICAL-c474t-62a642b08238f9ca642586770b94f0f51a7f35bc193be2a173b900c4822550e13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00438-020-01656-y$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00438-020-01656-y$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32172356$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yu, Dingwei</creatorcontrib><creatorcontrib>Li, Libei</creatorcontrib><creatorcontrib>Wei, Hengling</creatorcontrib><creatorcontrib>Yu, Shuxun</creatorcontrib><title>Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing</title><title>Molecular genetics and genomics : MGG</title><addtitle>Mol Genet Genomics</addtitle><addtitle>Mol Genet Genomics</addtitle><description>Genetic male sterility (GMS) facilitates hybrid seed production in crops including cotton (
Gossypium hirsutum
). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and transcriptome sequencing were performed to analyze miRNAs and their target genes during anther development in a GMS mutant (‘Dong A’) and its fertile wildtype (WT). A total of 80 known and 220 novel miRNAs were identified, 71 of which showed differential expressions during anther development. A further degradome sequencing revealed a total of 117 candidate target genes cleaved by 16 known and 36 novel miRNAs. Based on RNA-seq, 24, 11, and 21 predicted target genes showed expression correlations with the corresponding miRNAs at the meiosis, tetrad and uninucleate stages, respectively. In addition, a large number of differentially expressed genes were identified, most of which were involved in sucrose and starch metabolism, carbohydrate metabolism, and plant hormone signal transduction based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The results of our study provide valuable information for further functional investigations of the important miRNAs and target genes involved in genetic male sterility and advance our understanding of miRNA regulatory functions during cotton anther development.</description><subject>Animal Genetics and Genomics</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Carbohydrate metabolism</subject><subject>Cotton</subject><subject>Flowers - genetics</subject><subject>Flowers - growth & development</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genomes</subject><subject>Gossypium - genetics</subject><subject>Gossypium - growth & development</subject><subject>Gossypium hirsutum</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Male sterility</subject><subject>Meiosis</subject><subject>Metabolism</subject><subject>Microbial Genetics and Genomics</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Molecular modelling</subject><subject>Mutants</subject><subject>Mutation</subject><subject>Original</subject><subject>Original Article</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Infertility - genetics</subject><subject>Plant Proteins - genetics</subject><subject>Plants, Genetically Modified - genetics</subject><subject>Plants, Genetically Modified - growth & development</subject><subject>Signal transduction</subject><subject>Starch</subject><subject>Sucrose</subject><subject>Transcriptome</subject><issn>1617-4615</issn><issn>1617-4623</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9ks1u1DAUhSMEoqXwAiyQJTZsAv6J7ckGqaooVKpAQrC2HOd64sqJg-1MO0_Y18IzU4afBSvbut859175VNVLgt8SjOW7hHHDVjWmuMZEcFFvH1WnRBBZN4Kyx8c74SfVs5RuMCZSUPm0OmGUSMq4OK3ur3qYsrPO6OzChPTUozkG67yb1ihYNDoTw9fP52lf6p21EHcK7f0Wwd0cISXo0RomSKhf4k6mpzxARD1swId5LDjqIN8CFP89mZ1Bo_ZQpwzReUDjkoto38LlhG6d7_N2BmRCzmWqjdNocOuhzkMMy3qYl4zKTCjBjwUmU3o-r55Y7RO8eDjPqu-XH75dfKqvv3y8uji_rk0jm1wLqkVDO7yibGVbs3vwlZASd21jseVES8t4Z0jLOqCaSNa1GJtmRSnnGAg7q94ffOelG6E3ZbeovZqjG3XcqqCd-rsyuUGtw0ZJihlueTF482AQQxk-ZTW6ZMB7PUFYkqJMSiFbvkdf_4PehCVOZb1CtS3mvGlEoeiBKv-UUgR7HIZgtcuJOuRElZyofU7Utohe_bnGUfIrGAVgByDNuy-F-Lv3f2x_AmPDzqI</recordid><startdate>20200501</startdate><enddate>20200501</enddate><creator>Yu, Dingwei</creator><creator>Li, Libei</creator><creator>Wei, Hengling</creator><creator>Yu, Shuxun</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200501</creationdate><title>Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing</title><author>Yu, Dingwei ; Li, Libei ; Wei, Hengling ; Yu, Shuxun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-62a642b08238f9ca642586770b94f0f51a7f35bc193be2a173b900c4822550e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Carbohydrate metabolism</topic><topic>Cotton</topic><topic>Flowers - genetics</topic><topic>Flowers - growth & development</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Gene Expression Regulation, Plant</topic><topic>Genomes</topic><topic>Gossypium - genetics</topic><topic>Gossypium - growth & development</topic><topic>Gossypium hirsutum</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Male sterility</topic><topic>Meiosis</topic><topic>Metabolism</topic><topic>Microbial Genetics and Genomics</topic><topic>MicroRNAs</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>Molecular modelling</topic><topic>Mutants</topic><topic>Mutation</topic><topic>Original</topic><topic>Original Article</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Infertility - genetics</topic><topic>Plant Proteins - genetics</topic><topic>Plants, Genetically Modified - genetics</topic><topic>Plants, Genetically Modified - growth & development</topic><topic>Signal transduction</topic><topic>Starch</topic><topic>Sucrose</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Dingwei</creatorcontrib><creatorcontrib>Li, Libei</creatorcontrib><creatorcontrib>Wei, Hengling</creatorcontrib><creatorcontrib>Yu, Shuxun</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular genetics and genomics : MGG</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Dingwei</au><au>Li, Libei</au><au>Wei, Hengling</au><au>Yu, Shuxun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing</atitle><jtitle>Molecular genetics and genomics : MGG</jtitle><stitle>Mol Genet Genomics</stitle><addtitle>Mol Genet Genomics</addtitle><date>2020-05-01</date><risdate>2020</risdate><volume>295</volume><issue>3</issue><spage>645</spage><epage>660</epage><pages>645-660</pages><issn>1617-4615</issn><eissn>1617-4623</eissn><abstract>Genetic male sterility (GMS) facilitates hybrid seed production in crops including cotton (
Gossypium hirsutum
). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and transcriptome sequencing were performed to analyze miRNAs and their target genes during anther development in a GMS mutant (‘Dong A’) and its fertile wildtype (WT). A total of 80 known and 220 novel miRNAs were identified, 71 of which showed differential expressions during anther development. A further degradome sequencing revealed a total of 117 candidate target genes cleaved by 16 known and 36 novel miRNAs. Based on RNA-seq, 24, 11, and 21 predicted target genes showed expression correlations with the corresponding miRNAs at the meiosis, tetrad and uninucleate stages, respectively. In addition, a large number of differentially expressed genes were identified, most of which were involved in sucrose and starch metabolism, carbohydrate metabolism, and plant hormone signal transduction based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The results of our study provide valuable information for further functional investigations of the important miRNAs and target genes involved in genetic male sterility and advance our understanding of miRNA regulatory functions during cotton anther development.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>32172356</pmid><doi>10.1007/s00438-020-01656-y</doi><tpages>16</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Animal Genetics and Genomics Biochemistry Biomedical and Life Sciences Carbohydrate metabolism Cotton Flowers - genetics Flowers - growth & development Gene expression Gene Expression Profiling Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Genomes Gossypium - genetics Gossypium - growth & development Gossypium hirsutum High-Throughput Nucleotide Sequencing Human Genetics Life Sciences Male sterility Meiosis Metabolism Microbial Genetics and Genomics MicroRNAs MicroRNAs - genetics miRNA Molecular modelling Mutants Mutation Original Original Article Plant Genetics and Genomics Plant Infertility - genetics Plant Proteins - genetics Plants, Genetically Modified - genetics Plants, Genetically Modified - growth & development Signal transduction Starch Sucrose Transcriptome |
title | Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing |
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