AUTHOR=Fang Lu , Cheng Feng , Wu Jian , Wang Xiaowu 

TITLE=The Impact of Genome Triplication on Tandem Gene Evolution in Brassica rapa

JOURNAL=Frontiers in Plant Science

VOLUME=3

YEAR=2012

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2012.00261

DOI=10.3389/fpls.2012.00261

ISSN=1664-462X

ABSTRACT=<p>Whole genome duplication (WGD) and tandem duplication (TD) are both important modes of gene expansion. However, how WGD influences tandemly duplicated genes is not well studied. We used <italic>Brassica rapa</italic>, which has undergone an additional genome triplication (WGT) and shares a common ancestor with <italic>Arabidopsis thaliana</italic>, <italic>Arabidopsis lyrata</italic>, and <italic>Thellungiella parvula</italic>, to investigate the impact of genome triplication on tandem gene evolution. We identified 2,137, 1,569, 1,751, and 1,135 tandem gene arrays in <italic>B. rapa</italic>, <italic>A. thaliana</italic>, <italic>A. lyrata</italic>, and <italic>T. parvula</italic> respectively. Among them, 414 conserved tandem arrays are shared by the three species without WGT, which were also considered as existing in the diploid ancestor of <italic>B. rapa</italic>. Thus, after genome triplication, <italic>B. rapa</italic> should have 1,242 tandem arrays according to the 414 conserved tandems. Here, we found 400 out of the 414 tandems had at least one syntenic ortholog in the genome of <italic>B. rapa</italic>. Furthermore, 294 out of the 400 shared syntenic orthologs maintain tandem arrays (more than one gene for each syntenic hit) in <italic>B. rapa</italic>. For the 294 tandem arrays, we obtained 426 copies of syntenic paralogous tandems in the triplicated genome of <italic>B. rapa</italic>. In this study, we demonstrated that tandem arrays in <italic>B. rapa</italic> were dramatically fractionated after WGT when compared either to non-tandem genes in the <italic>B. rapa</italic> genome or to the tandem arrays in closely related species that have not experienced a recent whole genome polyploidization event.</p>