title: Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses.
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.
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Jinpeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Jiaxiang
authors.initials: J
authors.lastname: Yu
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Pengchuan
authors.initials: P
authors.lastname: Sun
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Yuxian
authors.initials: Y
authors.lastname: Li
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Ruiyan
authors.initials: R
authors.lastname: Xia
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Yinzhe
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Xuelian
authors.initials: X
authors.lastname: Ma
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Jigao
authors.initials: J
authors.lastname: Yu
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Nanshan
authors.initials: N
authors.lastname: Yang
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Tianyu
authors.initials: T
authors.lastname: Lei
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Zhenyi
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Weina
authors.initials: W
authors.lastname: Ge
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Song
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Xiaojian
authors.initials: X
authors.lastname: Liu
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Sangrong
authors.initials: S
authors.lastname: Sun
authors.affiliation: College of Science, North China University of Science and Technology Tangshan, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: College of Science, North China University of Science and Technology Tangshan, China.
authors.forename: Dianchuan
authors.initials: D
authors.lastname: Jin
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China.
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
keywords: chromosome; genome; grass; pineapple; rice