Dynamic Evolution of NLR Genes in Dalbergioids

Abstract

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species.

Keywords: NLR expansion; NLR genes; R genes gain and loss; allopolyploid; allotetraploids; contraction; novel resistance resources; peanut; wild Arachis species.

Figure 1

Horizontal bar plots illustrate the proper placement of four classes of NLRs genes indicated with different colors in different species of Adesmia, Dalbergia, and Pterocarpus clades.

Figure 2

Landscape of NLR genes using synteny and gene density analysis. (A) Synteny analysis of NLR genes from three species A. duranensis, A. evenia, and D. odorifera. (B) The NLRs genes are located on chromosomes denoted in vertical blue and red lines, inferring the gene density map between genome assemblies of Arachis, Dalbergia, and A. evenia species. These plot show placement of genes on linearized chromosomes that are joined together using a bin size of 5 kb.

Figure 3

Phylogenetic reconstruction of NLR gene identified from Dalbergioids species.

Figure 4

Gene orthologs and number of gene gains and loss analysis: (A,B) Venn diagrams illustrate the distribution of a number of shared and common genes regarding A- and B-related genome species. (C) Each node represents the number of genes, for instance, gene duplication is indicated in black font, and gene gain and loss are shown in green and red color, respectively.

Figure 5

Evaluation of historical NLR gene duplication in the genus of Dalbergia. All six species belonging to Dalbergioids with Ks values of their paralogs are represented. (A) X and Y axis indicating the Ks values and their frequencies. (B) Generalized Dalbergioids duplication pattern. (B) These boxplots show the Ks values between Dalbergia and Arachis species. A middle line represents the median of Ks.

Figure 6

Expression of NLR genes in Aeschynomene species. (A) The heatmap plot represents the expression of 50 NLR genes across 10 species of Aeschynomene during the rooting stage (day 7). (B) The bar plots show the variable cumulative gene expression of NLR in different species under the stress condition of drought. (C) The bar plot represents the number of genes expressed during this stage in different species.