Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication
Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRN...
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| Veröffentlicht in: | The Plant journal : for cell and molecular biology 2016-02, Vol.85 (3), p.396-409 |
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| creator | Liu, Tengfei Fang, Chao Ma, Yanming Shen, Yanting Li, Congcong Li, Qing Wang, Min Liu, Shulin Zhang, Jixiang Zhou, Zhengkui Yang, Rui Wang, Zheng Tian, Zhixi |
| description | Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication. |
| doi_str_mv | 10.1111/tpj.13113 |
| format | Article |
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Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication.</description><identifier>ISSN: 0960-7412</identifier><identifier>EISSN: 1365-313X</identifier><identifier>DOI: 10.1111/tpj.13113</identifier><identifier>PMID: 26714457</identifier><language>eng</language><publisher>England: Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology</publisher><subject>Biological Evolution ; coevolution ; co‐evolution ; Domestication ; Evolution, Molecular ; Genes ; Genetic Variation ; Genome, Plant - genetics ; Genomes ; Glycine max ; Glycine max - genetics ; Glycine soja ; microRNA ; microRNA target ; MicroRNAs ; MicroRNAs - genetics ; MIRNA gene ; population growth ; RNA, Plant - genetics ; soybean ; Soybeans ; surveys</subject><ispartof>The Plant journal : for cell and molecular biology, 2016-02, Vol.85 (3), p.396-409</ispartof><rights>2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd</rights><rights>2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.</rights><rights>Copyright © 2016 John Wiley & Sons Ltd and the Society for Experimental Biology</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Ftpj.13113$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Ftpj.13113$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27901,27902,45550,45551,46384,46808</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26714457$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Tengfei</creatorcontrib><creatorcontrib>Fang, Chao</creatorcontrib><creatorcontrib>Ma, Yanming</creatorcontrib><creatorcontrib>Shen, Yanting</creatorcontrib><creatorcontrib>Li, Congcong</creatorcontrib><creatorcontrib>Li, Qing</creatorcontrib><creatorcontrib>Wang, Min</creatorcontrib><creatorcontrib>Liu, Shulin</creatorcontrib><creatorcontrib>Zhang, Jixiang</creatorcontrib><creatorcontrib>Zhou, Zhengkui</creatorcontrib><creatorcontrib>Yang, Rui</creatorcontrib><creatorcontrib>Wang, Zheng</creatorcontrib><creatorcontrib>Tian, Zhixi</creatorcontrib><title>Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication</title><title>The Plant journal : for cell and molecular biology</title><addtitle>Plant J</addtitle><description>Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication.</description><subject>Biological Evolution</subject><subject>coevolution</subject><subject>co‐evolution</subject><subject>Domestication</subject><subject>Evolution, Molecular</subject><subject>Genes</subject><subject>Genetic Variation</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Glycine max</subject><subject>Glycine max - genetics</subject><subject>Glycine soja</subject><subject>microRNA</subject><subject>microRNA target</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MIRNA gene</subject><subject>population growth</subject><subject>RNA, Plant - genetics</subject><subject>soybean</subject><subject>Soybeans</subject><subject>surveys</subject><issn>0960-7412</issn><issn>1365-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1O3DAQx62qCJaPQ1-gWOLCJeCxHTs5IlS-xJdakHqzHMdJvU3ibZyA9sYj8Iw8Cd5d6IETvow185u_PfNH6BuQA4jncJhND4ABsC9oAkykCQP2-yuakFyQRHKgG2gzhCkhIJng62iDCgmcp3KC_p42vtANdt2DDYOr9eB8h32Fhz8WG__y9GwffDO-Z6_Of14f4dp2NmDdlbh1pveL1KD72g4Bl2PvuhoHPy-s7nDp24WsWcpuo7VKN8HuvMUtdH_y4-74LLm8OT0_PrpMKk4oSwyvCLPS0JRmoK0QaUmyFEpaGMFzm-WcAi0ryBkrcmqoSQFsrDFZ0YpBxrbQ_kp31vt_Y3xftS4Y2zS6s34MCjLCSEa5_AQqBXBJgLCI7n1Ap37suzjIkorfETmN1Pc3aixaW6pZ71rdz9X7xiNwuAIeXWPn_-tA1MJKFa1USyvV3e3F8hI7dlcdlfZK170L6v4XJSCinySlceBX8zuY9w</recordid><startdate>201602</startdate><enddate>201602</enddate><creator>Liu, Tengfei</creator><creator>Fang, Chao</creator><creator>Ma, Yanming</creator><creator>Shen, Yanting</creator><creator>Li, Congcong</creator><creator>Li, Qing</creator><creator>Wang, Min</creator><creator>Liu, Shulin</creator><creator>Zhang, Jixiang</creator><creator>Zhou, Zhengkui</creator><creator>Yang, Rui</creator><creator>Wang, Zheng</creator><creator>Tian, Zhixi</creator><general>Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology</general><general>Blackwell Publishing Ltd</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope></search><sort><creationdate>201602</creationdate><title>Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication</title><author>Liu, Tengfei ; Fang, Chao ; Ma, Yanming ; Shen, Yanting ; Li, Congcong ; Li, Qing ; Wang, Min ; Liu, Shulin ; Zhang, Jixiang ; Zhou, Zhengkui ; Yang, Rui ; Wang, Zheng ; Tian, Zhixi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-f4023-c4f03e7c25281ae665d0851d2bc649e894212df1933b92c2c511ebc637f2f3183</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Biological Evolution</topic><topic>coevolution</topic><topic>co‐evolution</topic><topic>Domestication</topic><topic>Evolution, Molecular</topic><topic>Genes</topic><topic>Genetic Variation</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Glycine max</topic><topic>Glycine max - genetics</topic><topic>Glycine soja</topic><topic>microRNA</topic><topic>microRNA target</topic><topic>MicroRNAs</topic><topic>MicroRNAs - genetics</topic><topic>MIRNA gene</topic><topic>population growth</topic><topic>RNA, Plant - genetics</topic><topic>soybean</topic><topic>Soybeans</topic><topic>surveys</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Tengfei</creatorcontrib><creatorcontrib>Fang, Chao</creatorcontrib><creatorcontrib>Ma, Yanming</creatorcontrib><creatorcontrib>Shen, Yanting</creatorcontrib><creatorcontrib>Li, Congcong</creatorcontrib><creatorcontrib>Li, Qing</creatorcontrib><creatorcontrib>Wang, Min</creatorcontrib><creatorcontrib>Liu, Shulin</creatorcontrib><creatorcontrib>Zhang, Jixiang</creatorcontrib><creatorcontrib>Zhou, Zhengkui</creatorcontrib><creatorcontrib>Yang, Rui</creatorcontrib><creatorcontrib>Wang, Zheng</creatorcontrib><creatorcontrib>Tian, Zhixi</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>The Plant journal : for cell and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Tengfei</au><au>Fang, Chao</au><au>Ma, Yanming</au><au>Shen, Yanting</au><au>Li, Congcong</au><au>Li, Qing</au><au>Wang, Min</au><au>Liu, Shulin</au><au>Zhang, Jixiang</au><au>Zhou, Zhengkui</au><au>Yang, Rui</au><au>Wang, Zheng</au><au>Tian, Zhixi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication</atitle><jtitle>The Plant journal : for cell and molecular biology</jtitle><addtitle>Plant J</addtitle><date>2016-02</date><risdate>2016</risdate><volume>85</volume><issue>3</issue><spage>396</spage><epage>409</epage><pages>396-409</pages><issn>0960-7412</issn><eissn>1365-313X</eissn><abstract>Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication.</abstract><cop>England</cop><pub>Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology</pub><pmid>26714457</pmid><doi>10.1111/tpj.13113</doi><tpages>14</tpages></addata></record> |
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| subjects | Biological Evolution coevolution co‐evolution Domestication Evolution, Molecular Genes Genetic Variation Genome, Plant - genetics Genomes Glycine max Glycine max - genetics Glycine soja microRNA microRNA target MicroRNAs MicroRNAs - genetics MIRNA gene population growth RNA, Plant - genetics soybean Soybeans surveys |
| title | Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication |
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