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author:("Wang, xiaohui")
1.  The Brassica genome 
doi:10.3389/fpls.2013.00148
PMCID: PMC3667235  PMID: 23755053
2.  Syntenic gene analysis between Brassica rapa and other Brassicaceae species 
Chromosomal synteny analysis is important in genome comparison to reveal genomic evolution of related species. Shared synteny describes genomic fragments from different species that originated from an identical ancestor. Syntenic genes are orthologs located in these syntenic fragments, so they often share similar functions. Syntenic gene analysis is very important in Brassicaceae species to share gene annotations and investigate genome evolution. Here we designed and developed a direct and efficient tool, SynOrths, to identify pairwise syntenic genes between genomes of Brassicaceae species. SynOrths determines whether two genes are a conserved syntenic pair based not only on their sequence similarity, but also by the support of homologous flanking genes. Syntenic genes between Arabidopsis thaliana and Brassica rapa, Arabidopsis lyrata and B. rapa, and Thellungiella parvula and B. rapa were then identified using SynOrths. The occurrence of genome triplication in B. rapa was clearly observed, many genes that were evenly distributed in the genomes of A. thaliana, A. lyrata, and T. parvula had three syntenic copies in B. rapa. Additionally, there were many B. rapa genes that had no syntenic orthologs in A. thaliana, but some of these had syntenic orthologs in A. lyrata or T. parvula. Only 5,851 genes in B. rapa had no syntenic counterparts in any of the other three species. These 5,851 genes could have originated after B. rapa diverged from these species. A tool for syntenic gene analysis between species of Brassicaceae was developed, SynOrths, which could be used to accurately identify syntenic genes in differentiated but closely-related genomes. With this tool, we identified syntenic gene sets between B. rapa and each of A. thaliana, A. lyrata, T. parvula. Syntenic gene analysis is important for not only the gene annotation of newly sequenced Brassicaceae genomes by bridging them to model plant A. thaliana, but also the study of genome evolution in these species.
doi:10.3389/fpls.2012.00198
PMCID: PMC3430884  PMID: 22969786
synteny; ortholog; Brassica rapa; Arabidopsis thaliana; Arabidopsis lyrata; Thellugiella parvula; Brassicaceae
3.  The Impact of Genome Triplication on Tandem Gene Evolution in Brassica rapa 
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.
doi:10.3389/fpls.2012.00261
PMCID: PMC3509317  PMID: 23226149
whole genome duplication; tandem duplication; tandem gene evolution; Brassica rapa; Arabidopsis thaliana; Arabidopsis lyrata; Thellungiella parvula

Results 1-3 (3)