title: Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa.
abstract: A genome triplication took place in the ancestor of Brassiceae species after the split of the Arabidopsis lineage. The postfragmentation and shuffling of the genome turned the ancestral hexaploid back to diploids and caused the radiation of Brassiceae species. The course of speciation was accompanied by the loss of duplicate genes and also influenced the evolution of retained genes. Of all the genes, those encoding NBS domains are typical R genes that confer resistance to invading pathogens. In this study, using the genome of Arabidopsis thaliana as a reference, we examined the loss/retention of orthologous NBS-encoding loci in the tripled Brassica rapa genome and discovered differential loss/retention frequencies. Further analysis indicated that loci of different retention ratios showed different evolutionary patterns. The loci of classesII and III (maintaining two and three syntenic loci, respectively, multi-loci) show sharper expansions by tandem duplications, have faster evolutionary rates and have more potential to be associated with novel gene functions. On the other hand, the loci that are retained at the minimal rate (keeping only one locus, class I, single locus) showed opposite patterns. Phylogenetic analysis indicated that recombination and translocation events were common among multi-loci in B. rapa, and differential evolutionary patterns between multi- and single-loci are likely the consequence of recombination. Investigations towards other gene families demonstrated different evolutionary characteristics between different gene families. The evolution of genes is more likely determined by the property of each gene family, and the whole genome triplication provided only a specific condition.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: ping9223@163.com.
authors.forename: Ping
authors.initials: P
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: zhuqingshao@126.com.
authors.forename: Zhu-Qing
authors.initials: ZQ
authors.lastname: Shao
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: wxz900810@gmail.com.
authors.forename: Xun-Zong
authors.initials: XZ
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: wangqiang1997@gmail.com.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: binwang@nju.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China. Electronic address: chenjq@nju.edu.cn.
authors.forename: Jian-Qun
authors.initials: JQ
authors.lastname: Chen
authors.affiliation: Jiangsu Provincial Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu Province, China. Electronic address: hangyueyu@gmail.com.
authors.forename: Yue-Yu
authors.initials: YY
authors.lastname: Hang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China; Jiangsu Provincial Key Laboratory for Plant Ex Situ Conservation, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu Province, China. Electronic address: xuejy@nju.edu.cn.
authors.forename: Jia-Yu
authors.initials: JY
authors.lastname: Xue
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011003:Ploidies; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D004268:DNA-Binding Proteins; D010940:Plant Proteins
keywords: Evolutionary pattern; Gene loss/retention; NBS-encoding genes; Polyploidy