Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass
The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass ( Dactylis glomerata L.), one of the top four economically important perennial forage grasse...
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| Veröffentlicht in: | Molecular biology reports 2020-03, Vol.47 (3), p.1845-1857 |
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| creator | Xu, Xiaoheng Feng, Guangyan Huang, Linkai Yang, Zhongfu Liu, Qiuxu Shuai, Yang Zhang, Xinquan |
| description | The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass (
Dactylis glomerata
L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46
GRAS
genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and
Brachypodium distachyon
. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or
Arabidopsis
classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of
DgGRAS
genes at mature and seeding stage. And we found that
DgGRAS17
played an important role in the growth and development no matter what stage it was at.
DgGRAS5
,
DgGRAS28
,
DgGRAS31
,
DgGRAS42
and
DgGRAS44
got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of
GRAS
genes. |
| doi_str_mv | 10.1007/s11033-020-05279-9 |
| format | Article |
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Dactylis glomerata
L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46
GRAS
genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and
Brachypodium distachyon
. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or
Arabidopsis
classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of
DgGRAS
genes at mature and seeding stage. And we found that
DgGRAS17
played an important role in the growth and development no matter what stage it was at.
DgGRAS5
,
DgGRAS28
,
DgGRAS31
,
DgGRAS42
and
DgGRAS44
got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of
GRAS
genes.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-05279-9</identifier><identifier>PMID: 32026320</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Amino Acid Motifs ; Animal Anatomy ; Animal Biochemistry ; Biomedical and Life Sciences ; Chromosome Mapping - methods ; Chromosomes, Plant - genetics ; Dactylis ; Dactylis - genetics ; Dactylis - growth & development ; Evolution, Molecular ; Gene Expression Profiling - methods ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Genes ; Genomes ; Histology ; Homology ; Life Sciences ; Morphology ; Multigene Family ; Original Article ; Phylogenetics ; Phylogeny ; Plant growth ; Plant Proteins - chemistry ; Plant Proteins - genetics ; Seeding ; Transcription factors ; Transcription Factors - chemistry ; Transcription Factors - genetics</subject><ispartof>Molecular biology reports, 2020-03, Vol.47 (3), p.1845-1857</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Molecular Biology Reports is a copyright of Springer, (2020). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-de544dd3957b277a86865f5a017324b1d68e54502257db9f0549cb2369723b23</citedby><cites>FETCH-LOGICAL-c375t-de544dd3957b277a86865f5a017324b1d68e54502257db9f0549cb2369723b23</cites><orcidid>0000-0002-1433-9510</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-020-05279-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-05279-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32026320$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xu, Xiaoheng</creatorcontrib><creatorcontrib>Feng, Guangyan</creatorcontrib><creatorcontrib>Huang, Linkai</creatorcontrib><creatorcontrib>Yang, Zhongfu</creatorcontrib><creatorcontrib>Liu, Qiuxu</creatorcontrib><creatorcontrib>Shuai, Yang</creatorcontrib><creatorcontrib>Zhang, Xinquan</creatorcontrib><title>Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass (
Dactylis glomerata
L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46
GRAS
genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and
Brachypodium distachyon
. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or
Arabidopsis
classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of
DgGRAS
genes at mature and seeding stage. And we found that
DgGRAS17
played an important role in the growth and development no matter what stage it was at.
DgGRAS5
,
DgGRAS28
,
DgGRAS31
,
DgGRAS42
and
DgGRAS44
got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of
GRAS
genes.</description><subject>Amino Acid Motifs</subject><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes, Plant - genetics</subject><subject>Dactylis</subject><subject>Dactylis - genetics</subject><subject>Dactylis - growth & development</subject><subject>Evolution, Molecular</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genomes</subject><subject>Histology</subject><subject>Homology</subject><subject>Life Sciences</subject><subject>Morphology</subject><subject>Multigene Family</subject><subject>Original Article</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant growth</subject><subject>Plant Proteins - chemistry</subject><subject>Plant Proteins - genetics</subject><subject>Seeding</subject><subject>Transcription factors</subject><subject>Transcription Factors - chemistry</subject><subject>Transcription Factors - genetics</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kU9vGyEQxVHVqHHSfoEcIqReegjpAMuye4ysxolkKVLrO2IX1sHdPw6zq8Tfvjh2U6mHHGCQ-L3HDI-QCw7XHEB_R85BSgYCGCihS1Z-IDOutGRZqYuPZAYSOMsKxU_JGeIGADKu1SdyKgWIPG0z8nvh-6Hz7Dk4T9Pqx9CE2o5h6K8ojnGqxynaltretjsMmA6O-pdt9IiJods4NKH1SIeGLn7e_KJr33va2C60Oxp6OsT60Ua3jhbxMzlpbIv-y7Gek9Xtj9X8ji0fFvfzmyWrpVYjc15lmXOyVLoSWtsiL3LVKAtcS5FV3OVFIhQIobSrygZUVtaVkHmphUz1nHw72KbeniaPo-kC1r5tbe-HCY2QSiQN5JDQr_-hm2GKadQ9pUFzLlWeKHGg6jggRt-YbQydjTvDweyTMIckTErCvCZhyiS6PFpPVefdm-Tv1ydAHgBMV_3ax39vv2P7B6cJkuA</recordid><startdate>20200301</startdate><enddate>20200301</enddate><creator>Xu, Xiaoheng</creator><creator>Feng, Guangyan</creator><creator>Huang, Linkai</creator><creator>Yang, Zhongfu</creator><creator>Liu, Qiuxu</creator><creator>Shuai, Yang</creator><creator>Zhang, Xinquan</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><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>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</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>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1433-9510</orcidid></search><sort><creationdate>20200301</creationdate><title>Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass</title><author>Xu, Xiaoheng ; Feng, Guangyan ; Huang, Linkai ; Yang, Zhongfu ; Liu, Qiuxu ; Shuai, Yang ; Zhang, Xinquan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-de544dd3957b277a86865f5a017324b1d68e54502257db9f0549cb2369723b23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amino Acid Motifs</topic><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Chromosome Mapping - 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Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xu, Xiaoheng</au><au>Feng, Guangyan</au><au>Huang, Linkai</au><au>Yang, Zhongfu</au><au>Liu, Qiuxu</au><au>Shuai, Yang</au><au>Zhang, Xinquan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2020-03-01</date><risdate>2020</risdate><volume>47</volume><issue>3</issue><spage>1845</spage><epage>1857</epage><pages>1845-1857</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass (
Dactylis glomerata
L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46
GRAS
genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and
Brachypodium distachyon
. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or
Arabidopsis
classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of
DgGRAS
genes at mature and seeding stage. And we found that
DgGRAS17
played an important role in the growth and development no matter what stage it was at.
DgGRAS5
,
DgGRAS28
,
DgGRAS31
,
DgGRAS42
and
DgGRAS44
got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of
GRAS
genes.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>32026320</pmid><doi>10.1007/s11033-020-05279-9</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-1433-9510</orcidid></addata></record> |
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| subjects | Amino Acid Motifs Animal Anatomy Animal Biochemistry Biomedical and Life Sciences Chromosome Mapping - methods Chromosomes, Plant - genetics Dactylis Dactylis - genetics Dactylis - growth & development Evolution, Molecular Gene Expression Profiling - methods Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Genes Genomes Histology Homology Life Sciences Morphology Multigene Family Original Article Phylogenetics Phylogeny Plant growth Plant Proteins - chemistry Plant Proteins - genetics Seeding Transcription factors Transcription Factors - chemistry Transcription Factors - genetics |
| title | Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass |
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