Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis
<p>Abstract</p> <p>Background</p> <p>Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so...
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| Format: | Article |
| Language: | English |
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BMC
2010-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/121 |
| _version_ | 1818238310327255040 |
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| author | Itoh Takeshi Sakai Hiroaki |
| author_facet | Itoh Takeshi Sakai Hiroaki |
| author_sort | Itoh Takeshi |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of <it>Oryza sativa </it>ssp. <it>japonica </it>with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, <it>O. rufipogon </it>and <it>O. nivara</it>, and an African rice species, <it>O. glaberrima</it>.</p> <p>Results</p> <p>We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the <it>japonica </it>genome, suggesting that a substantial number of genes have been lost in the <it>japonica </it>rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, <it>O. sativa </it>has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain.</p> <p>Conclusion</p> <p>We found that the <it>O. sativa </it>lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close relatives of cultivated rice have the potential to restore the lost traits.</p> |
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| format | Article |
| id | doaj.art-1666c10737824776a30d45d8ddb73731 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T12:39:37Z |
| publishDate | 2010-02-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-1666c10737824776a30d45d8ddb737312022-12-22T00:24:14ZengBMCBMC Genomics1471-21642010-02-0111112110.1186/1471-2164-11-121Massive gene losses in Asian cultivated rice unveiled by comparative genome analysisItoh TakeshiSakai Hiroaki<p>Abstract</p> <p>Background</p> <p>Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of <it>Oryza sativa </it>ssp. <it>japonica </it>with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, <it>O. rufipogon </it>and <it>O. nivara</it>, and an African rice species, <it>O. glaberrima</it>.</p> <p>Results</p> <p>We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the <it>japonica </it>genome, suggesting that a substantial number of genes have been lost in the <it>japonica </it>rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, <it>O. sativa </it>has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain.</p> <p>Conclusion</p> <p>We found that the <it>O. sativa </it>lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close relatives of cultivated rice have the potential to restore the lost traits.</p>http://www.biomedcentral.com/1471-2164/11/121 |
| spellingShingle | Itoh Takeshi Sakai Hiroaki Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis BMC Genomics |
| title | Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis |
| title_full | Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis |
| title_fullStr | Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis |
| title_full_unstemmed | Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis |
| title_short | Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis |
| title_sort | massive gene losses in asian cultivated rice unveiled by comparative genome analysis |
| url | http://www.biomedcentral.com/1471-2164/11/121 |
| work_keys_str_mv | AT itohtakeshi massivegenelossesinasiancultivatedriceunveiledbycomparativegenomeanalysis AT sakaihiroaki massivegenelossesinasiancultivatedriceunveiledbycomparativegenomeanalysis |