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.
Highlights
The genomes of species from Brassicaceae are composed of 24 basic genomic blocks, A–X (24 GBs, called the ancestral karyotypes, AK) (Schranz et al, 2006), as detected by studies using comparative chromosomal painting (CCP) (Mandakova and Lysak, 2008), and directly observed in Arabidopsis thaliana (Initiative, 2000), and the newly sequenced genomes of Arabidopsis lyrata (Hu et al, 2011), Brassica rapa (Wang et al, 2011), and Thellungiella parvula (Dassanayake et al, 2011)
To share gene annotations between B. rapa and the other annotated genomes specially for A. thaliana and dig for clues of the B. rapa genome evolution, we developed a tool, SynOrths, which is well suited for detecting syntenic orthologs between closely related species, and applied it to the synteny analysis between B. rapa and other sequenced genomes from Brassicaceae: the model plant A. thaliana, A. lyrata, and T. parvula
DEVELOPMENT OF THE SYNORTHS TOOL TO IDENTIFY GENE PAIRS WITH SYNTENIC RELATIONSHIPS A tool named SynOrths was developed to identify syntenic genes based on the protein sequences of B. rapa and other related species
Summary
The genomes of species from Brassicaceae are composed of 24 basic genomic blocks, A–X (24 GBs, called the ancestral karyotypes, AK) (Schranz et al, 2006), as detected by studies using comparative chromosomal painting (CCP) (Mandakova and Lysak, 2008), and directly observed in Arabidopsis thaliana (Initiative, 2000), and the newly sequenced genomes of Arabidopsis lyrata (Hu et al, 2011), Brassica rapa (Wang et al, 2011), and Thellungiella parvula (Dassanayake et al, 2011). Along with drastic genome changes, gene contents have rapidly evolved (Cheng et al, 2012; Tang et al, 2012). As they share a common AK, the chromosomal synteny relationship among these genomes is considered to be well preserved despite the long time for evolution following the divergence of these species (Tang et al, 2008; Cheng et al, 2012). Shared synteny describes genomic fragments from different species that originated from a certain common ancestor (Lyons et al, 2008). Syntenic genes are orthologs located in these syntenic fragments, so they often share similar functions, and we can be highly confident when sharing their functional annotation information
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