Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L
The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid e...
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| creator | Shen, Shulin Sun, Fujun Zhu, Meichen Chen, Si Guan, Mingwei Chen, Rui Tang, Fang Yin, Nengwen Xu, Xinfu Tang, Zhanglin Li, Jiana Lu, Kun Qu, Cunmin |
| description | The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species. |
| doi_str_mv | 10.1371/journal.pone.0234411 |
| format | Article |
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The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0234411</identifier><identifier>PMID: 32511257</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Agronomy ; Analysis ; Biological evolution ; Biology and Life Sciences ; Biotechnology ; Brassica ; Brassica napus ; Chromosomes ; Computer and Information Sciences ; Developmental stages ; Engineering research ; Evolution ; Evolutionary genetics ; Functional analysis ; Gene expression ; Gene sequencing ; Genes ; Genetic aspects ; Genomes ; Genomics ; Identification and classification ; Localization ; Methods ; Morphology ; Organs ; Pattern analysis ; Phylogenetics ; Phylogeny ; Physiological aspects ; Polyploidy ; Proteins ; Rapeseed ; Regulatory genes ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA sequencing ; Seeds</subject><ispartof>PloS one, 2020-06, Vol.15 (6), p.e0234411-e0234411</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Shen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Shen et al 2020 Shen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c570t-798f78dde13b48b2984fec7d8377db720257c69cba6e59f182d5a3e08f6f971b3</citedby><cites>FETCH-LOGICAL-c570t-798f78dde13b48b2984fec7d8377db720257c69cba6e59f182d5a3e08f6f971b3</cites><orcidid>0000-0003-2413-2350</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7279594/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7279594/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids></links><search><creatorcontrib>Shen, Shulin</creatorcontrib><creatorcontrib>Sun, Fujun</creatorcontrib><creatorcontrib>Zhu, Meichen</creatorcontrib><creatorcontrib>Chen, Si</creatorcontrib><creatorcontrib>Guan, Mingwei</creatorcontrib><creatorcontrib>Chen, Rui</creatorcontrib><creatorcontrib>Tang, Fang</creatorcontrib><creatorcontrib>Yin, Nengwen</creatorcontrib><creatorcontrib>Xu, Xinfu</creatorcontrib><creatorcontrib>Tang, Zhanglin</creatorcontrib><creatorcontrib>Li, Jiana</creatorcontrib><creatorcontrib>Lu, Kun</creatorcontrib><creatorcontrib>Qu, Cunmin</creatorcontrib><title>Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L</title><title>PloS one</title><description>The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.</description><subject>Agronomy</subject><subject>Analysis</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Brassica</subject><subject>Brassica napus</subject><subject>Chromosomes</subject><subject>Computer and Information Sciences</subject><subject>Developmental stages</subject><subject>Engineering research</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Functional analysis</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Identification and classification</subject><subject>Localization</subject><subject>Methods</subject><subject>Morphology</subject><subject>Organs</subject><subject>Pattern 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identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L</title><author>Shen, Shulin ; Sun, Fujun ; Zhu, Meichen ; Chen, Si ; Guan, Mingwei ; Chen, Rui ; Tang, Fang ; Yin, Nengwen ; Xu, Xinfu ; Tang, Zhanglin ; Li, Jiana ; Lu, Kun ; Qu, Cunmin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c570t-798f78dde13b48b2984fec7d8377db720257c69cba6e59f182d5a3e08f6f971b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agronomy</topic><topic>Analysis</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Biotechnology</topic><topic>Brassica</topic><topic>Brassica napus</topic><topic>Chromosomes</topic><topic>Computer and Information Sciences</topic><topic>Developmental stages</topic><topic>Engineering research</topic><topic>Evolution</topic><topic>Evolutionary 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Rui</au><au>Tang, Fang</au><au>Yin, Nengwen</au><au>Xu, Xinfu</au><au>Tang, Zhanglin</au><au>Li, Jiana</au><au>Lu, Kun</au><au>Qu, Cunmin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L</atitle><jtitle>PloS one</jtitle><date>2020-06-08</date><risdate>2020</risdate><volume>15</volume><issue>6</issue><spage>e0234411</spage><epage>e0234411</epage><pages>e0234411-e0234411</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>32511257</pmid><doi>10.1371/journal.pone.0234411</doi><orcidid>https://orcid.org/0000-0003-2413-2350</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Agronomy Analysis Biological evolution Biology and Life Sciences Biotechnology Brassica Brassica napus Chromosomes Computer and Information Sciences Developmental stages Engineering research Evolution Evolutionary genetics Functional analysis Gene expression Gene sequencing Genes Genetic aspects Genomes Genomics Identification and classification Localization Methods Morphology Organs Pattern analysis Phylogenetics Phylogeny Physiological aspects Polyploidy Proteins Rapeseed Regulatory genes Research and Analysis Methods Ribonucleic acid RNA RNA sequencing Seeds |
| title | Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-03T07%3A57%3A06IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20identification%20AINTEGUMENTA-like%20(AIL)%20genes%20in%20Brassica%20species%20and%20expression%20patterns%20during%20reproductive%20development%20in%20Brassica%20napus%20L&rft.jtitle=PloS%20one&rft.au=Shen,%20Shulin&rft.date=2020-06-08&rft.volume=15&rft.issue=6&rft.spage=e0234411&rft.epage=e0234411&rft.pages=e0234411-e0234411&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0234411&rft_dat=%3Cgale_plos_%3EA626087018%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2410687904&rft_id=info:pmid/32511257&rft_galeid=A626087018&rft_doaj_id=oai_doaj_org_article_22287d647c9b4d5abf527e1cd524280e&rfr_iscdi=true |