Lozano Roberto, Hamblin Martha T, Prochnik Simon, Jannink Jean-Luc
Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.
Institute for Genomic Diversity, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA.
BMC Genomics. 2015 May 7;16(1):360. doi: 10.1186/s12864-015-1554-9.
Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop.
With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor.
This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.
植物抗性基因（R基因）存在于大家族中，通常包含一个核苷酸结合位点结构域和一个富含亮氨酸的重复结构域，称为NBS-LRR。木薯（Manihot esculenta）的基因组序列是分析该作物抗性基因基因组组织的宝贵资源。
通过搜索Pfam结构域并人工整理木薯基因注释，我们鉴定出228个NBS-LRR类型基因和99个部分NBS基因。这些基因几乎占预测基因总数的1%，并与其他植物物种的蛋白质具有高度序列相似性。此外，34个基因含有N端类toll/白细胞介素（TIR）结构域，128个基因含有N端卷曲螺旋（CC）结构域。327个R基因中的63%分布在染色体上的39个簇中。这些簇大多是同源的，包含来自最近共同祖先的NBS-LRR。
本研究深入了解了木薯基因组中NBS-LRR基因的进化；系统发育和定位信息可能有助于进一步表征这些预测R基因的功能。
