Syntenic gene analysis between Brassica rapa and other Brassicaceae species

Abstract

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.

Keywords: Arabidopsis lyrata; Arabidopsis thaliana; Brassica rapa; Brassicaceae; Thellugiella parvula; ortholog; synteny.

Figure 1

The principles of syntenic gene identification in SynOrths. When determining whether two genes are under synteny, both the sequence homology of the two genes themselves and their flanking genes are considered. (A) Syntenic genes in the same direction in each genome. (B) Two syntenic genes located in inverted syntenic fragments.

Figure 2

Parameter estimation in SynOrths. The number of query (B. rapa) flanking genes [5, 20, 60, 100], the number of reference (A. thaliana) flanking genes [10, 40, 100, 150], and the threshold of the flanking genes' support ratio [0.1, 0.2, 0.4, 0.8] were set to run SynOrths. The bars indicate the proportions of syntenic genes identified out of 38,161 B. rapa genes, “%detected synteny” means percent of identified syntenic genes to the 38,161 B. rapa genes. The bar with a red border is the run with parameters NumQ = 20, NumR = 100, and RatioQR = 0.2; SynOrths returned stable and relatively more syntenic genes under these parameters.

Figure 3

Syntenic genes identified by SynOrths between B. rapa and A. thaliana, A. lyrata, or T. parvula. For each segment in A. thaliana, A. lyrata, or T. parvula, there were three syntenic copies observed in B. rapa, which clearly reflected the genome triplication experienced by B. rapa. Colors of the dots represent for the 24 ancestral blocks of Brassicaceae species, which has been defined previously (Schranz et al., 2006).