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Variation Patterns of NLr Clusters in Arabidopsis thaliana Genomes

Plant Communications 2020年第4期1卷 129-143页

作者： rachelle r.q.lee Eunyoung Chae Department of Biological Sciences National University of SingaporeSingapore 117558Singapore

The nucleotide-binding domain and leucine-rich repeat(NLr)gene family is highly expanded in the plant lineage with extensive sequence and structure *** survey the landscape of NLr expansion,we mined the published long-read data generated by the resistance gene enrichment sequencing of 64 diverse Arabidopsis thaliana *** found that the hot spots of massive multi-gene NLr cluster expansion did not typically span the whole cluster;instead,they were restricted to a handful of,or only one,dominant radiation(s).All sequences in such a radiation were distinct from other genes in the cluster but not from each other in the clade,making it difficult to assign trustworthy reference-based orthologies when multiple reference genes were present in the ***,NLr genes can be broadly divided into two types:radiating or high-fidelity,where high-fidelity genes are well conserved and well separated from other clades.A similar distinction could be made for NLr clusters,depending on whether cluster size was determined primarily by extensive radiation or the presence of numerous high-fidelity *** also identified groups of well-conserved NLr clades that were missing from the Columbia-0 reference *** suggests that the classification of NLrs using gene IDs from a single reference accession can rarely capture all major paralogs in a cluster accurately and representatively and that a referenceagnostic perspective is required to properly characterize these additional ***,we present a quantitative visualization method for differentiating these situations in a given clade of interest.

关键词： NLr cluster evolution phylogenetics disease resistance plant immunity

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