Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
Front Plant Sci. 2012 Aug 30;3:198. doi: 10.3389/fpls.2012.00198. eCollection 2012.
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.
染色体同线性分析在比较基因组中揭示相关物种的基因组进化非常重要。共有同线性描述了来自不同物种的基因组片段，这些片段起源于同一个祖先。同线性基因是位于这些同线性片段中的直系同源基因，因此它们通常具有相似的功能。同线性基因分析在十字花科物种中非常重要，可以共享基因注释并研究基因组进化。在这里，我们设计并开发了一种直接有效的工具 SynOrths，用于鉴定十字花科物种基因组之间的成对同线性基因。SynOrths 不仅根据基因序列的相似性，还根据同源侧翼基因的支持来确定两个基因是否是保守的同线性对。然后使用 SynOrths 鉴定了拟南芥和油菜、拟南芥和油菜、以及小立碗藓和油菜之间的同线性基因。在油菜中明显观察到基因组三倍体的发生，在拟南芥、拟南芥和小立碗藓基因组中均匀分布的许多基因在油菜中有三个同线性拷贝。此外，油菜中有许多基因在拟南芥中没有同线性直系同源基因，但其中一些在拟南芥或小立碗藓中有同线性直系同源基因。只有油菜中的 5851 个基因在其他三个物种中没有同线性对应基因。这些 5851 个基因可能是油菜与这些物种分化后产生的。开发了一种用于十字花科物种之间同线性基因分析的工具 SynOrths，它可以用于准确鉴定分化但密切相关的基因组中的同线性基因。使用该工具，我们鉴定了油菜与拟南芥、拟南芥和小立碗藓之间的同线性基因集。同线性基因分析不仅对通过与模式植物拟南芥桥接新测序的十字花科基因组的基因注释很重要，而且对这些物种的基因组进化研究也很重要。
