Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice
The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, whi...
Saved in:
Published in | Yíchuán Vol. 37; no. 12; p. 1228 |
---|---|
Main Authors | , , , |
Format | Journal Article |
Language | Chinese |
Published |
China
01.12.2015
|
Subjects | |
Online Access | Get more information |
Cover
Loading…
Abstract | The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools. These members could be classified into 5 subfamilies (I~V) based on the evolutionary relationship and domain characteristics. Clustering analyses of the Trihelix family in rice, Arabidopsis, Brachypodium distachyom and Sorghum bicolor showed that each species contained different members of subfamily although the classification of the Trihelix family were consistent in these four species, which indicated that the differentiation of the Trihelix gene family occur earlier than that of these species. The conserved motifs in the Trihelix family of rice analyzed using the MEME program were highly consistent with the results of clustering analyses. Intraspecific and interspecific chromosomal replication in partial Trihelix family members were found to exist in rice and between rice and other species through chromosome replication analysis. Microarray data analysis revealed diverse expression patterns of Trihelix family genes in different tissues of rice or in response to six different phytohormones. Moreover, 20 members of the Trihelix transcription factor family were found to interact with other proteins in rice using RiceFRIEND online database analysis. Therefore, our results preliminarily identified the evolution, chromosome distribution and replication, expression patterns, phytohormones response of the Trihelix transcription factor family and the interaction between trihelix family proteins and other proteins in rice, which will provide a basis to further reveal the molecular evolution and biological function of the Trihelix transcription factor family. |
---|---|
AbstractList | The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools. These members could be classified into 5 subfamilies (I~V) based on the evolutionary relationship and domain characteristics. Clustering analyses of the Trihelix family in rice, Arabidopsis, Brachypodium distachyom and Sorghum bicolor showed that each species contained different members of subfamily although the classification of the Trihelix family were consistent in these four species, which indicated that the differentiation of the Trihelix gene family occur earlier than that of these species. The conserved motifs in the Trihelix family of rice analyzed using the MEME program were highly consistent with the results of clustering analyses. Intraspecific and interspecific chromosomal replication in partial Trihelix family members were found to exist in rice and between rice and other species through chromosome replication analysis. Microarray data analysis revealed diverse expression patterns of Trihelix family genes in different tissues of rice or in response to six different phytohormones. Moreover, 20 members of the Trihelix transcription factor family were found to interact with other proteins in rice using RiceFRIEND online database analysis. Therefore, our results preliminarily identified the evolution, chromosome distribution and replication, expression patterns, phytohormones response of the Trihelix transcription factor family and the interaction between trihelix family proteins and other proteins in rice, which will provide a basis to further reveal the molecular evolution and biological function of the Trihelix transcription factor family. |
Author | Yang, Li-ming Ji, Jian-hui Zhou, Ying-jun Wu, He-he |
Author_xml | – sequence: 1 givenname: Jian-hui surname: Ji fullname: Ji, Jian-hui organization: Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture &Environment Protection(JCIC-RMAEP), School of Life Sciences, Huaiyin Normal University, Huai'an 223300, China – sequence: 2 givenname: Ying-jun surname: Zhou fullname: Zhou, Ying-jun organization: Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture &Environment Protection(JCIC-RMAEP), School of Life Sciences, Huaiyin Normal University, Huai'an 223300, China – sequence: 3 givenname: He-he surname: Wu fullname: Wu, He-he organization: Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture &Environment Protection(JCIC-RMAEP), School of Life Sciences, Huaiyin Normal University, Huai'an 223300, China – sequence: 4 givenname: Li-ming surname: Yang fullname: Yang, Li-ming organization: Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture &Environment Protection(JCIC-RMAEP), School of Life Sciences, Huaiyin Normal University, Huai'an 223300, China |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26704948$$D View this record in MEDLINE/PubMed |
BookMark | eNo1jz1PwzAYhD0U0VK6MiL_gRT7jT-SEVVQkCqxZK9s541qlDiRkwrSX49VYLq756ST7o4sQh-QkAfOtlxBUTx9bmd3uWy5zHipFmTFQOZZqTUsyWYcvWWMFSoxfUuWoDQTpShWxO4x9B1mX75GaoJp59GPydS0OQc3-T4hOkSs_TXQvqHTCWkV_Qlb_02naMLooh-ubWPc1McknW9n6gON3uE9uWlMO-LmT9eken2pdm_Z4WP_vns-ZI5rPmXSWmCibnIlreAGNCC6sqylUAIt19JAw0xqBHNCSJXngKBNuiTBSYQ1efydHc62w_o4RN-ZOB__v8IPXLFYtA |
CitedBy_id | crossref_primary_10_3389_fgene_2021_727674 |
ContentType | Journal Article |
DBID | CGR CUY CVF ECM EIF NPM |
DOI | 10.16288/j.yczz.15-196 |
DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) |
DatabaseTitleList | MEDLINE |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
DeliveryMethod | no_fulltext_linktorsrc |
Discipline | Biology |
ExternalDocumentID | 26704948 |
Genre | English Abstract Journal Article |
GroupedDBID | -01 2B. 2C. 5XA 5XB 92E 92I ACGFS ALMA_UNASSIGNED_HOLDINGS CCEZO CCVFK CGR CUY CVF CW9 DU5 ECM EIF NPM OK1 TCJ TGP U1G U5K |
ID | FETCH-LOGICAL-c171t-5bb204df365b41a272eec99d5464eb175a2f0a41a40c4456332e27a62552c5e2 |
ISSN | 0253-9772 |
IngestDate | Wed Jun 21 13:36:24 EDT 2023 |
IsPeerReviewed | false |
IsScholarly | true |
Issue | 12 |
Language | Chinese |
LinkModel | OpenURL |
MergedId | FETCHMERGED-LOGICAL-c171t-5bb204df365b41a272eec99d5464eb175a2f0a41a40c4456332e27a62552c5e2 |
PMID | 26704948 |
ParticipantIDs | pubmed_primary_26704948 |
PublicationCentury | 2000 |
PublicationDate | 2015-12-00 |
PublicationDateYYYYMMDD | 2015-12-01 |
PublicationDate_xml | – month: 12 year: 2015 text: 2015-12-00 |
PublicationDecade | 2010 |
PublicationPlace | China |
PublicationPlace_xml | – name: China |
PublicationTitle | Yíchuán |
PublicationTitleAlternate | Yi Chuan |
PublicationYear | 2015 |
SSID | ssib000862537 ssj0039441 ssib001528691 ssib006576199 ssib002264282 ssib002806135 ssib051376046 |
Score | 2.0385852 |
Snippet | The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification... |
SourceID | pubmed |
SourceType | Index Database |
StartPage | 1228 |
SubjectTerms | Amino Acid Sequence Gene Expression Profiling Gene Expression Regulation, Plant Genome, Plant Molecular Sequence Data Multigene Family Oryza - chemistry Oryza - classification Oryza - genetics Oryza - metabolism Phylogeny Plant Proteins - chemistry Plant Proteins - genetics Plant Proteins - metabolism Sequence Alignment Transcription Factors - chemistry Transcription Factors - genetics Transcription Factors - metabolism |
Title | Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice |
URI | https://www.ncbi.nlm.nih.gov/pubmed/26704948 |
Volume | 37 |
hasFullText | |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwELa2RUhcUHm_5QNXl7VjJ9kjooVqBT0toj1VedhKEJtdVRuV7q9nxo_EW0A8LpETR9mN58vM57FnhpDXpoSvz-Qpq01ZM8nzghVFkjI4w6i0GdhcDBT-dJqefJbzM3U2mVzF0SWb8rDa_jKu5H-kCtdArhgl-w-SHR4KF6AN8oUjSBiOfyXjD7pbLTW7amtcBPDZRdATjtbKO_nWl7gUE3gh0szFZdvob-13LA_RjVrDVd4JHg8Mc_Hb4gJ3PbeL6kdV09sGH2A1tzsC5gA01vTt6Ipe9VbBg3FkX_vh7i-9M3esGTB17p3WH1u2DKbUeyK4inZ1OIUlVMKAT-5oV5fSJaBIRLqSCxcW_pMSxwrIVotfV9vtIf6OK3obSXS9tCIVaWbz2_y590ZS7dC1R_ayHBXjaezkgVmeilgbUJw8TimEsccijxejkRSNajFV6BsaWKLiuPEIZ92OIGAosi3kGIbL5xLF136z89KYqdr_0RuzHst-Fgfkrp-20LcOg_fIZNvcJ7ddIdPrB6SMkEgDEqFR0xGJdEQiXRkKSKQBiXQHidQhkTok0rajiMSHZPH-ePHuhPnqHaziGd8wVZZiKmuTpKqUvBCZ0LqazWolUwkEIVOFMNMCeuS0kkDjk0RokRUw9EpUSotHZL9bdfoJobqGu2ujlC6MlEky4_AgoFGYmEomqXlKHruxuVi7DC0XYdSe_bbnObkzQvgFuWVAJeiXwC835SuLhh-kUW6U |
link.rule.ids | 786 |
linkProvider | National Library of Medicine |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Genome-wide+analysis+and+functional+prediction+of+the+Trihelix+transcription+factor+family+in+rice&rft.jtitle=Y%C3%ADchu%C3%A1n&rft.au=Ji%2C+Jian-hui&rft.au=Zhou%2C+Ying-jun&rft.au=Wu%2C+He-he&rft.au=Yang%2C+Li-ming&rft.date=2015-12-01&rft.issn=0253-9772&rft.volume=37&rft.issue=12&rft.spage=1228&rft_id=info:doi/10.16288%2Fj.yczz.15-196&rft_id=info%3Apmid%2F26704948&rft_id=info%3Apmid%2F26704948&rft.externalDocID=26704948 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0253-9772&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0253-9772&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0253-9772&client=summon |