Abstract
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 Brassica rapa, which has undergone an additional genome triplication (WGT) and shares a common ancestor with Arabidopsis thaliana, Arabidopsis lyrata, and Thellungiella parvula, 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 B. rapa, A. thaliana, A. lyrata, and T. parvula 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 B. rapa. Thus, after genome triplication, B. rapa 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 B. rapa. Furthermore, 294 out of the 400 shared syntenic orthologs maintain tandem arrays (more than one gene for each syntenic hit) in B. rapa. For the 294 tandem arrays, we obtained 426 copies of syntenic paralogous tandems in the triplicated genome of B. rapa. In this study, we demonstrated that tandem arrays in B. rapa were dramatically fractionated after WGT when compared either to non-tandem genes in the B. rapa genome or to the tandem arrays in closely related species that have not experienced a recent whole genome polyploidization event.
Highlights
Gene copy number can be expanded through many ways, including whole genome duplication (WGD), tandem duplication (TD), segmental duplication, and gene transposition duplication
The distribution of gene numbers in tandem arrays was not significantly different among the four species. Among these tandem gene arrays, 414 were syntenic tandem arrays shared among A. thaliana, A. lyrata, and T. parvula (Figure 2; Table 1 in Supplementary Material)
This set of shared tandem gene arrays was used as the set of presumed ancestral tandem arrays, to investigate their evolution in B. rapa after whole genome triplication (WGT)
Summary
Gene copy number can be expanded through many ways, including whole genome duplication (WGD), tandem duplication (TD), segmental duplication, and gene transposition duplication. Among these four kinds of duplications, WGD played an important role in the evolution of eukaryotes and was well documented in many sequenced genomes (Semon and Wolfe, 2007; Edger and Pires, 2009). A singlecopy gene in an ancestral angiosperm a million years ago could have expanded into a large gene family in recent species by WGD (Semon and Wolfe, 2007). Genes expanded by TD are always distributed together as a cluster in chromosomes
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