Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max)
Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the im...
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| description | Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species.
Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.
Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications. |
| doi_str_mv | 10.1186/s12870-014-0282-7 |
| format | Article |
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Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.
Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.</description><identifier>ISSN: 1471-2229</identifier><identifier>EISSN: 1471-2229</identifier><identifier>DOI: 10.1186/s12870-014-0282-7</identifier><identifier>PMID: 25348509</identifier><language>eng</language><publisher>England: BioMed Central</publisher><subject>Cyclophilins - genetics ; Databases, Genetic ; Fabaceae - genetics ; Genome, Plant - genetics ; Genome-Wide Association Study ; Glycine max ; Glycine max - genetics ; Introns - genetics ; Multigene Family ; Open Reading Frames - genetics ; Organ Specificity ; Peptidylprolyl Isomerase - genetics ; Plant Proteins - genetics ; Protein Structure, Tertiary ; Untranslated Regions - genetics</subject><ispartof>BMC plant biology, 2014-10, Vol.14 (1), p.282-282, Article 282</ispartof><rights>2014 Mainali et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Mainali et al.; licensee BioMed Central Ltd. 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c460t-97ad16142f07cb362504d1fa1b39d7daa79e6ac342878626e7b32bbb86e573a33</citedby><cites>FETCH-LOGICAL-c460t-97ad16142f07cb362504d1fa1b39d7daa79e6ac342878626e7b32bbb86e573a33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220052/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220052/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25348509$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mainali, Hemanta Raj</creatorcontrib><creatorcontrib>Chapman, Patrick</creatorcontrib><creatorcontrib>Dhaubhadel, Sangeeta</creatorcontrib><title>Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max)</title><title>BMC plant biology</title><addtitle>BMC Plant Biol</addtitle><description>Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species.
Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.
Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.</description><subject>Cyclophilins - genetics</subject><subject>Databases, Genetic</subject><subject>Fabaceae - genetics</subject><subject>Genome, Plant - genetics</subject><subject>Genome-Wide Association Study</subject><subject>Glycine max</subject><subject>Glycine max - genetics</subject><subject>Introns - genetics</subject><subject>Multigene Family</subject><subject>Open Reading Frames - genetics</subject><subject>Organ Specificity</subject><subject>Peptidylprolyl Isomerase - genetics</subject><subject>Plant Proteins - genetics</subject><subject>Protein Structure, Tertiary</subject><subject>Untranslated Regions - genetics</subject><issn>1471-2229</issn><issn>1471-2229</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><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>eNqNkUFLwzAUx4MoTqcfwIsUvOihmveSJu1FkKGbMPCi55C26YykzWw2td_elulQT56S8H7vz3v5EXIC9BIgFVcBMJU0psBjiinGcoccAJcQI2K2--M-IochvFAKMuXZPhlhwnia0OyAzKam8bWJ321pIt1o1wUbIl9Fk65wfvlsnW2ihWlMVOnaui7qn8F3udFNdD51XWH7Uq0_Lo7IXqVdMMdf55g83d0-Tmbx_GF6P7mZxwUXdBVnUpcggGNFZZEzgQnlJVQacpaVstRaZkbogvF-s1SgMDJnmOd5KkwimWZsTK43uct1XpuyMM2q1U4tW1vrtlNeW_W70thntfBviiNSmmAfcP4V0PrXtQkrVdtQGOd0Y_w6KBCCsowJYP9AE-QUMzmgZ3_QF79u-_8cKKRcIqSyp2BDFa0PoTXVdm6galCqNkpVr1QNStXQc_pz4W3Ht0P2CcyOmwI</recordid><startdate>20141029</startdate><enddate>20141029</enddate><creator>Mainali, Hemanta Raj</creator><creator>Chapman, Patrick</creator><creator>Dhaubhadel, Sangeeta</creator><general>BioMed Central</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>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20141029</creationdate><title>Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max)</title><author>Mainali, Hemanta Raj ; Chapman, Patrick ; Dhaubhadel, Sangeeta</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c460t-97ad16142f07cb362504d1fa1b39d7daa79e6ac342878626e7b32bbb86e573a33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Cyclophilins - genetics</topic><topic>Databases, Genetic</topic><topic>Fabaceae - genetics</topic><topic>Genome, Plant - genetics</topic><topic>Genome-Wide Association Study</topic><topic>Glycine max</topic><topic>Glycine max - genetics</topic><topic>Introns - genetics</topic><topic>Multigene Family</topic><topic>Open Reading Frames - genetics</topic><topic>Organ Specificity</topic><topic>Peptidylprolyl Isomerase - genetics</topic><topic>Plant Proteins - genetics</topic><topic>Protein Structure, Tertiary</topic><topic>Untranslated Regions - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mainali, Hemanta Raj</creatorcontrib><creatorcontrib>Chapman, Patrick</creatorcontrib><creatorcontrib>Dhaubhadel, Sangeeta</creatorcontrib><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>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</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 One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</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>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>Agricultural Science Database</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>Publicly Available Content Database</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>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC plant biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mainali, Hemanta Raj</au><au>Chapman, Patrick</au><au>Dhaubhadel, Sangeeta</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max)</atitle><jtitle>BMC plant biology</jtitle><addtitle>BMC Plant Biol</addtitle><date>2014-10-29</date><risdate>2014</risdate><volume>14</volume><issue>1</issue><spage>282</spage><epage>282</epage><pages>282-282</pages><artnum>282</artnum><issn>1471-2229</issn><eissn>1471-2229</eissn><abstract>Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species.
Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.
Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.</abstract><cop>England</cop><pub>BioMed Central</pub><pmid>25348509</pmid><doi>10.1186/s12870-014-0282-7</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Cyclophilins - genetics Databases, Genetic Fabaceae - genetics Genome, Plant - genetics Genome-Wide Association Study Glycine max Glycine max - genetics Introns - genetics Multigene Family Open Reading Frames - genetics Organ Specificity Peptidylprolyl Isomerase - genetics Plant Proteins - genetics Protein Structure, Tertiary Untranslated Regions - genetics |
| title | Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max) |
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