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 TITLE=Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses JOURNAL=Frontiers in Genetics VOLUME=7 YEAR=2016 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2016.00174 DOI=10.3389/fgene.2016.00174 ISSN=1664-8021 ABSTRACT=

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.