Abstract
BackgroundPlant disease resistance (R) genes are evolving rapidly and play a critical role in the innate immune system of plants. The nucleotide binding sites-leucine rich repeat (NBS-LRR) genes are one of the largest classes in plant R genes. Previous studies have focused on the NBS-LRR genes from one or several species of different genera, and the sequenced genomes of the genus Fragaria offer the opportunity to study the evolutionary processes of these R genes among the closely related species.ResultsIn this study, 325, 155, 190, 187, and 133 NBS-LRRs were discovered from F. x ananassa, F. iinumae, F. nipponica, F. nubicola, and F. orientalis, respectively. Together with the 144 NBS-LRR genes from F. vesca, a total of 1134 NBS-LRRs containing 866 multi-genes comprised 184 gene families across the six Fragaria genomes. Extremely short branch lengths and shallow nodes were widely present in the phylogenetic tree constructed with all of the NBS-LRR genes of the six strawberry species. The identities of the orthologous genes were highly significantly greater than those of the paralogous genes, while the Ks ratios of the former were very significantly lower than those of the latter in all of the NBS-LRR gene families. In addition, the Ks and Ka/Ks values of the TIR-NBS-LRR genes (TNLs) were significantly greater than those of the non-TIR-NBS-LRR genes (non-TNLs). Furthermore, the expression patterns of the NBS-LRR genes revealed that the same gene expressed differently under different genetic backgrounds in response to pathogens.ConclusionsThese results, combined with the shared hotspot regions of the duplicated NBS-LRRs on the chromosomes, indicated that the lineage-specific duplication of the NBS-LRR genes occurred before the divergence of the six Fragaria species. The Ks and Ka/Ks ratios suggested that the TNLs are more rapidly evolving and driven by stronger diversifying selective pressures than the non-TNLs.
Highlights
Plant disease resistance (R) genes are evolving rapidly and play a critical role in the innate immune system of plants
Identification of nucleotide binding sites-leucine rich repeat (NBS-leucine-rich repeat (LRR)) genes in six Fragaria species According to searches for nucleotide-binding site (NBS)-LRRs by using BLAST and Hidden Markov Model (HMM) methods, a total of 1134 NBS-LRR genes were detected from the six Fragaria genomes, and 325, 155, 190, 187, and 133 NBS-LRRs from F. x ananassa, F. iinumae, F. nipponica, F. nubicola, and F. orientalis, respectively (Table 1)
In the four diploid Fragaria species, the NBSLRR gene numbers normally ranged in a narrow scope, from 144 (F. vesca) to 190 (F. nipponica), because their similar genome sizes were close to the true genome values (~ 200 Mb) [25]
Summary
Plant disease resistance (R) genes are evolving rapidly and play a critical role in the innate immune system of plants. Previous studies have focused on the NBS-LRR genes from one or several species of different genera, and the sequenced genomes of the genus Fragaria offer the opportunity to study the evolutionary processes of these R genes among the closely related species. The R genes have such a broad spectrum of resistance, they only encode five types of proteins, in which NBS-LRR (nucleotide binding sitesleucine-rich repeat) genes are the largest class of plant R genes [3]. The recently released whole genome sequences of F. x ananassa and four wild species, F.iinumae, F. nipponica, F. nubicola and F. orientalis, provide an opportunity to conduct the genome-wide identification of NBS-LRR genes and uncover the evolutionary processes of these R genes among the Fragaria genomes [25] in relation to F. vesca, the reference strawberry species [14]
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