Genome-wide patterns of large-size presence/ absence variants in sorghum
The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L...
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| Veröffentlicht in: | Journal of integrative plant biology 2014, Vol.56 (1), p.24-37 |
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| container_title | Journal of integrative plant biology |
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| creator | Zhang, Li-Min Luo, Hong Liu, Zhi-Quan Zhao, Yi Luo, Jing-Chu Hao, Dong-Yun Jing, Hai-Chun |
| description | The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding. |
| doi_str_mv | 10.1111/jipb.12121 |
| format | Article |
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However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.</description><identifier>ISSN: 1672-9072</identifier><identifier>EISSN: 1744-7909</identifier><identifier>DOI: 10.1111/jipb.12121</identifier><identifier>PMID: 24428208</identifier><language>eng</language><publisher>China (Republic : 1949- ): Blackwell Publishing Ltd</publisher><subject>Breeding ; Chromosomes, Plant - genetics ; Crosses, Genetic ; DNA Transposable Elements - genetics ; Gene Ontology ; Genes, Plant - genetics ; genetic diversity ; Genetic Variation ; Genome Size - genetics ; Genome, Plant - genetics ; genomics ; Inbreeding ; Inheritance Patterns - genetics ; Molecular Sequence Annotation ; presence/absence variants ; Retroelements - genetics ; Sequence Analysis, DNA ; Sorghum - genetics ; Sorghum bicolour ; 全基因组 ; 变种 ; 基因组变异 ; 大尺寸 ; 植物基因组 ; 测序工作 ; 结构变异 ; 高粱属</subject><ispartof>Journal of integrative plant biology, 2014, Vol.56 (1), p.24-37</ispartof><rights>2013 Institute of Botany, Chinese Academy of Sciences</rights><rights>2013 Institute of Botany, Chinese Academy of Sciences.</rights><rights>Copyright © Wanfang Data Co. 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All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/94176A/94176A.jpg</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjipb.12121$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjipb.12121$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,781,785,1418,4025,27928,27929,27930,45579,45580</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24428208$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Li-Min</creatorcontrib><creatorcontrib>Luo, Hong</creatorcontrib><creatorcontrib>Liu, Zhi-Quan</creatorcontrib><creatorcontrib>Zhao, Yi</creatorcontrib><creatorcontrib>Luo, Jing-Chu</creatorcontrib><creatorcontrib>Hao, Dong-Yun</creatorcontrib><creatorcontrib>Jing, Hai-Chun</creatorcontrib><title>Genome-wide patterns of large-size presence/ absence variants in sorghum</title><title>Journal of integrative plant biology</title><addtitle>Journal of Integrative Plant Biology</addtitle><description>The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.</description><subject>Breeding</subject><subject>Chromosomes, Plant - genetics</subject><subject>Crosses, Genetic</subject><subject>DNA Transposable Elements - genetics</subject><subject>Gene Ontology</subject><subject>Genes, Plant - genetics</subject><subject>genetic diversity</subject><subject>Genetic Variation</subject><subject>Genome Size - genetics</subject><subject>Genome, Plant - genetics</subject><subject>genomics</subject><subject>Inbreeding</subject><subject>Inheritance Patterns - genetics</subject><subject>Molecular Sequence Annotation</subject><subject>presence/absence variants</subject><subject>Retroelements - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Sorghum - genetics</subject><subject>Sorghum bicolour</subject><subject>全基因组</subject><subject>变种</subject><subject>基因组变异</subject><subject>大尺寸</subject><subject>植物基因组</subject><subject>测序工作</subject><subject>结构变异</subject><subject>高粱属</subject><issn>1672-9072</issn><issn>1744-7909</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kE9v1DAQxS0EoqVw4QOgcEDiknb8L7aPbAVpUUWL1Iqj5TjO1kvibO2EbfvpcXe3tQ9-8vzejOYh9BHDMc7nZOXXzTEm-b5Ch1gwVgoF6nXWlSClAkEO0LuUVgBUQkXeogPCGJEE5CE6q10YB1dufOuKtZkmF0Mqxq7oTVy6MvnH_B1dcsG6k8I0W1H8M9GbMKXChyKNcXk7D-_Rm870yX3Yv0fo5sf369Oz8uKyPj_9dlFaKikuO8E73HDBBbTAJAVljWjbtrEVWMO5tco2XDrV0E5azEnbEaisNI61xnJBj9CXXd-NCZ0JS70a5xjyRP24uW8IYAYYgGfu645bx_FudmnSg0_W9b0JbpyTxiwHgwUlKqOf9ujcDK7V6-gHEx_0c0oZwPuZvncPL3UM-il__ZS_3uavf55fLbYqe8qdx6fJ3b94TPyrK0EF139-1Vouarb4DbUmmf-84-3tGJZ3Pm_27GGyUkwpRv8D1J2Rqg</recordid><startdate>2014</startdate><enddate>2014</enddate><creator>Zhang, Li-Min</creator><creator>Luo, Hong</creator><creator>Liu, Zhi-Quan</creator><creator>Zhao, Yi</creator><creator>Luo, Jing-Chu</creator><creator>Hao, Dong-Yun</creator><creator>Jing, Hai-Chun</creator><general>Blackwell Publishing Ltd</general><general>The Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China%college of Life Sciences, Peking University, Beijing 100871, China%Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130012, China</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W94</scope><scope>WU4</scope><scope>~WA</scope><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope></search><sort><creationdate>2014</creationdate><title>Genome-wide patterns of large-size presence/ absence variants in sorghum</title><author>Zhang, Li-Min ; Luo, Hong ; Liu, Zhi-Quan ; Zhao, Yi ; Luo, Jing-Chu ; Hao, Dong-Yun ; Jing, Hai-Chun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3831-f75f1b57570d048309ca7dddbc60ca55cc9cb58e9b3f8c152df206c8ae4dac573</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Breeding</topic><topic>Chromosomes, Plant - genetics</topic><topic>Crosses, Genetic</topic><topic>DNA Transposable Elements - genetics</topic><topic>Gene Ontology</topic><topic>Genes, Plant - genetics</topic><topic>genetic diversity</topic><topic>Genetic Variation</topic><topic>Genome Size - genetics</topic><topic>Genome, Plant - genetics</topic><topic>genomics</topic><topic>Inbreeding</topic><topic>Inheritance Patterns - genetics</topic><topic>Molecular Sequence Annotation</topic><topic>presence/absence variants</topic><topic>Retroelements - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Sorghum - genetics</topic><topic>Sorghum bicolour</topic><topic>全基因组</topic><topic>变种</topic><topic>基因组变异</topic><topic>大尺寸</topic><topic>植物基因组</topic><topic>测序工作</topic><topic>结构变异</topic><topic>高粱属</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Li-Min</creatorcontrib><creatorcontrib>Luo, Hong</creatorcontrib><creatorcontrib>Liu, Zhi-Quan</creatorcontrib><creatorcontrib>Zhao, Yi</creatorcontrib><creatorcontrib>Luo, Jing-Chu</creatorcontrib><creatorcontrib>Hao, Dong-Yun</creatorcontrib><creatorcontrib>Jing, Hai-Chun</creatorcontrib><collection>中文科技期刊数据库</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>中文科技期刊数据库-7.0平台</collection><collection>中文科技期刊数据库-自然科学</collection><collection>中文科技期刊数据库-自然科学-生物科学</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><collection>Wanfang Data Journals - Hong Kong</collection><collection>WANFANG Data Centre</collection><collection>Wanfang Data Journals</collection><collection>万方数据期刊 - 香港版</collection><collection>China Online Journals (COJ)</collection><collection>China Online Journals (COJ)</collection><jtitle>Journal of integrative plant biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Li-Min</au><au>Luo, Hong</au><au>Liu, Zhi-Quan</au><au>Zhao, Yi</au><au>Luo, Jing-Chu</au><au>Hao, Dong-Yun</au><au>Jing, Hai-Chun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide patterns of large-size presence/ absence variants in sorghum</atitle><jtitle>Journal of integrative plant biology</jtitle><addtitle>Journal of Integrative Plant Biology</addtitle><date>2014</date><risdate>2014</risdate><volume>56</volume><issue>1</issue><spage>24</spage><epage>37</epage><pages>24-37</pages><issn>1672-9072</issn><eissn>1744-7909</eissn><abstract>The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.</abstract><cop>China (Republic : 1949- )</cop><pub>Blackwell Publishing Ltd</pub><pmid>24428208</pmid><doi>10.1111/jipb.12121</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Journal of integrative plant biology, 2014, Vol.56 (1), p.24-37 |
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| source | MEDLINE; Access via Wiley Online Library; Alma/SFX Local Collection |
| subjects | Breeding Chromosomes, Plant - genetics Crosses, Genetic DNA Transposable Elements - genetics Gene Ontology Genes, Plant - genetics genetic diversity Genetic Variation Genome Size - genetics Genome, Plant - genetics genomics Inbreeding Inheritance Patterns - genetics Molecular Sequence Annotation presence/absence variants Retroelements - genetics Sequence Analysis, DNA Sorghum - genetics Sorghum bicolour 全基因组 变种 基因组变异 大尺寸 植物基因组 测序工作 结构变异 高粱属 |
| title | Genome-wide patterns of large-size presence/ absence variants in sorghum |
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