AUTHOR=Zhang Yan-Mei , Chen Min , Sun Ling , Wang Yue , Yin Jianmei , Liu Jia , Sun Xiao-Qin , Hang Yue-Yu 

TITLE=Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00484

DOI=10.3389/fgene.2020.00484

ISSN=1664-8021

ABSTRACT=<p><italic>Dioscorea rotundata</italic> is an important food crop that is mainly cultivated in subtropical regions of the world. <italic>D. rotundata</italic> is frequently infected by various pathogens during its lifespan, which results in a substantial economic loss in terms of yield and quality. The disease resistance gene (<italic>R</italic> gene) profile of <italic>D. rotundata</italic> is largely unknown, which has greatly hampered molecular study of disease resistance in this species. <italic>Nucleotide-binding site–leucine-rich repeat</italic> (<italic>NBS-LRR</italic>) genes are the largest group of plant <italic>R</italic> genes, and they play important roles in plant defense responses to various pathogens. In this study, 167 <italic>NBS-LRR</italic> genes were identified from the <italic>D. rotundata</italic> genome. Subsequently, one gene was assigned to the <italic>resistance to powdery mildew8</italic> (<italic>RPW8</italic>)<italic>-NBS-LRR</italic> (<italic>RNL</italic>) subclass and the other 166 genes to the <italic>coiled coil</italic> (<italic>CC</italic>)<italic>-NBS-LRR</italic> (<italic>CNL</italic>) subclass. None of the <italic>Toll/interleukin-1 receptor</italic> (<italic>TIR</italic>)<italic>-NBS-LRR</italic> (<italic>TNL</italic>) genes were detected in the genome. Among them, 124 genes are located in 25 multigene clusters and 43 genes are singletons. Tandem duplication serves as the major force for the cluster arrangement of <italic>NBS-LRR</italic> genes. Segmental duplication was detected for 18 <italic>NBS-LRR</italic> genes, although no whole-genome duplication has been documented for the species. Phylogenetic analysis revealed that <italic>D. rotundata NBS-LRR</italic> genes share 15 ancestral lineages with <italic>Arabidopsis thaliana</italic> genes. The <italic>NBS-LRR</italic> gene number increased by more than a factor of 10 during <italic>D. rotundata</italic> evolution. A conservatively evolved ancestral lineage was identified from <italic>D. rotundata</italic>, which is orthologs to the <italic>Arabidopsis RPM1</italic> gene. Transcriptome analysis for four different tissues of <italic>D. rotundata</italic> revealed a low expression of most <italic>NBS-LRR</italic> genes, with the tuber and leaf displaying a relatively high <italic>NBS-LRR</italic> gene expression than the stem and flower. Overall, this study provides a complete set of <italic>NBS-LRR</italic> genes for <italic>D. rotundata</italic>, which may serve as a fundamental resource for mining functional <italic>NBS-LRR</italic> genes against various pathogens.</p>