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Abstract:
Plant health is an essential component of crop yield. Plant researchers are thus driven to understand the molecular basis of plant immunity and resistance. Resistance genes are key players in a plant’s fight against the tremendous diversity of pathogenic attackers. Nucleotide-binding and leucine-rich repeat (NLR) containing genes represent one of the most important resistance gene families in plants. They detect pathogenic effectors that try to interfere with cellular processes and induce resistance responses. As a result of an evolutionary arms race between plants and pathogens, NLRs have been shaped by repeated ancient and ongoing duplication events, with many NLR genes being found in complex clusters. High variability between strains has been inferred from comparisons of individual clusters for a small number of strains, but the true extent of species-wide NLR variation is unknown – even for the model plant Arabidopsis thaliana. Simple short read based re-sequencing approaches have largely failed to answer this question because of the excessive sequence and copy number variation between accessions. We have used instead NLR-sequence enrichment followed by long-read sequencing to assemble and annotate individual NLR’omes of a set of 65 A. thaliana accessions representing the global diversity of the species. Unexpectedly, a large fraction of genes was conserved and could be recovered by interrogating only a limited number of accessions. Some NLRs, however, are restricted to single accessions, or just a few accessions. Expression data from the 1001 Transcriptomes project was used to detect putative active NLRs that could be candidates for functional studies. We will discuss how rare NLRs, domain architecture differences, within-gene indels and SNPs contribute to NLR’ome variation. The structural description of the pan NLR’ome is a first step towards understanding the evolution of this important gene family in A. thaliana.
