Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetrapl...
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| Format: | Online |
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Frontiers Media S.A.
2016
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047885/ |
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pubmed-50478852016-10-18 Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses Wang, Jinpeng Yu, Jiaxiang Sun, Pengchuan Li, Yuxian Xia, Ruiyan Liu, Yinzhe Ma, Xuelian Yu, Jigao Yang, Nanshan Lei, Tianyu Wang, Zhenyi Wang, Li Ge, Weina Song, Xiaoming Liu, Xiaojian Sun, Sangrong Liu, Tao Jin, Dianchuan Pan, Yuxin Wang, Xiyin Genetics Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n = 2x = 14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor. Frontiers Media S.A. 2016-10-04 /pmc/articles/PMC5047885/ /pubmed/27757123 http://dx.doi.org/10.3389/fgene.2016.00174 Text en Copyright © 2016 Wang, Yu, Sun, Li, Xia, Liu, Ma, Yu, Yang, Lei, Wang, Wang, Ge, Song, Liu, Sun, Liu, Jin, Pan and Wang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
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NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Wang, Jinpeng Yu, Jiaxiang Sun, Pengchuan Li, Yuxian Xia, Ruiyan Liu, Yinzhe Ma, Xuelian Yu, Jigao Yang, Nanshan Lei, Tianyu Wang, Zhenyi Wang, Li Ge, Weina Song, Xiaoming Liu, Xiaojian Sun, Sangrong Liu, Tao Jin, Dianchuan Pan, Yuxin Wang, Xiyin |
| spellingShingle |
Wang, Jinpeng Yu, Jiaxiang Sun, Pengchuan Li, Yuxian Xia, Ruiyan Liu, Yinzhe Ma, Xuelian Yu, Jigao Yang, Nanshan Lei, Tianyu Wang, Zhenyi Wang, Li Ge, Weina Song, Xiaoming Liu, Xiaojian Sun, Sangrong Liu, Tao Jin, Dianchuan Pan, Yuxin Wang, Xiyin Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| author_facet |
Wang, Jinpeng Yu, Jiaxiang Sun, Pengchuan Li, Yuxian Xia, Ruiyan Liu, Yinzhe Ma, Xuelian Yu, Jigao Yang, Nanshan Lei, Tianyu Wang, Zhenyi Wang, Li Ge, Weina Song, Xiaoming Liu, Xiaojian Sun, Sangrong Liu, Tao Jin, Dianchuan Pan, Yuxin Wang, Xiyin |
| author_sort |
Wang, Jinpeng |
| title |
Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| title_short |
Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| title_full |
Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| title_fullStr |
Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| title_full_unstemmed |
Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses |
| title_sort |
comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses |
| description |
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n = 2x = 14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor. |
| publisher |
Frontiers Media S.A. |
| publishDate |
2016 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047885/ |
| _version_ |
1613670592462979072 |