Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes inArabidopsis     

Abstract

Plants, like animals, use several lines of defense against pathogen attack. Prominent among genes that confer disease resistance are those encoding nucleotide-binding site-leucine-rich repeat (NB-LRR) proteins. Likely due to selection pressures caused by pathogens, NB-LRR genes are the most variable gene family in plants, but there appear to be species-specific limits to the number of NB-LRR genes in a genome. Allelic diversity within an individual is also increased by obligatory outcrossing, which leads to genome-wide heterozygosity. In this study, we compared the NB-LRR gene complement of the selfer Arabidopsis thaliana and its outcrossing close relative Arabidopsis lyrata. We then complemented and contrasted the interspecific patterns with studies of NB-LRR diversity within A. thaliana. Three important insights are as follows: (1) that both species have similar numbers of NB-LRR genes; (2) that loci with single NB-LRR genes are less variable than tandem arrays; and (3) that presenceabsence polymorphisms within A. thaliana are not strongly correlated with the presence or absence of orthologs in A. lyrata. Although A. thaliana individuals are mostly homozygous and thus potentially less likely to suffer from aberrant interaction of NB-LRR proteins with newly introduced alleles, the number of NB-LRR genes is similar to that in A. lyrata. In intraspecific and interspecific comparisons, NB-LRR genes are also more variable than receptor-like protein genes. Finally, in contrast to Drosophila, there is a clearly positive relationship between interspecific divergence and intraspecific polymorphisms.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

“…We ran GOWINDA with 100,000 simulations in 'gene' mode, assuming that only SNPs located inside a gene are associated with the corresponding gene (-gene-definition 'gene'). Additionally to GO_SLIM terms from TAIR10 we created and tested GO term for NB-LRR gene family previously identified 72 .…”

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

“…However, the relative contributions of recent and ancient expansions to the abundance of NBS genes in modern plant genomes remain elusive. Recent studies report the evolutionary analyses of NBS genes across multiple species in a plant family (Cannon et al, 2002;Guo et al, 2011;Luo et al, 2012;Lin et al, 2013;Shao et al, 2014;Zhang et al, 2016). While studies in Brassicaceae and Poaceae both revealed abundant and recent losses of NBS genes in various species after the divergence of these two families, a study involving Fabaceae has suggested the opposite scenario in which all surveyed species recently underwent a multitude of NBS expansions (Luo et al, 2012;Shao et al, 2014;Zhang et al, 2016).…”

Natural Variation in Small Molecule–Induced TIR-NB-LRR Signaling Induces Root Growth Arrest via EDS1- and PAD4-Complexed R Protein VICTR inArabidopsis

“…The genome of Arabidopsis thaliana contains ;150 NB-LRR genes, and up to 600 genes are found in rice (Oryza sativa; Kadota et al, 2010). The presence of many polymorphisms in NB-LRR genes has been proposed as a diversification process against rapidly evolving pathogens (Tian et al, 2003;Guo et al, 2011). In fact, NB-LRR genes represent the most variable plant gene family (Weigel, 2012).…”