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. 2020 May 7:11:484.
doi: 10.3389/fgene.2020.00484. eCollection 2020.

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

Yan-Mei Zhang  1 , Min Chen  1 , Ling Sun  1 , Yue Wang  1 , Jianmei Yin  2 , Jia Liu  1 , Xiao-Qin Sun  1 , Yue-Yu Hang  1
Affiliations

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

Yan-Mei Zhang et al. Front Genet. .

Abstract

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

Keywords: Dioscorea rotundata; NBS-LRR genes; R gene; genome-wide analysis; pathogen defense.

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Figures

FIGURE 1
FIGURE 1
Identification and classification of D. rotundata NBS-LRR genes based on protein domain structure. 167 NBS-LRR genes were identified from the D. rotundata genome and classified into six groups with different domain compositions and arrangements. The identified integrated domains (IDs) are also listed as a word cloud.
FIGURE 2
FIGURE 2
Chromosomal distribution of D. rotundata NBS-LRR genes. The 167 identified NBS-LRR genes are plotted against the D. rotundata chromosomes based on their physical locations retrieved from the GFF3 file. NBS-LRR genes within an interval of less than 250 kb were treated as a cluster (Ameline-Torregrosa et al., 2008).
FIGURE 3
FIGURE 3
Syntenic relationship of the 18 segmental-duplicated NBS-LRR genes.
FIGURE 4
FIGURE 4
Phylogeny of RNL and CNL genes of D. rotundata, T. zeylanicus, and A. thaliana. The phylogeny was constructed based on the conserved NBS domain of CNL and RNL genes from D. rotundata, T. zeylanicus and A. thaliana. Branch support values obtained from a UFBoot2 test are labeled on basal nodes. Predicted ancestral lineages in the common ancestor of the three species (C1–C15) and ancestral lineages in the common ancestor of D. rotundata and T. zeylanicus (D1–D35) are indicated at the right of the phylogeny. The CNL-A, CNL-B, and CNL-C and D lineages are labeled according to Meyers et al. (2003).
FIGURE 5
FIGURE 5
Expression pattern of D. rotundata NBS-LRR genes. (A) Heatmap of the expression of 167 NBS-LRR genes in four different plant tissues. (B) Average expression of 167 NBS-LRR genes in the four tissues. (C) Distribution of the top expression tissue for the 167 NBS-LRR genes.
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