Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Abstract

Research conducted: Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in pine but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Methods: Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Key results: Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. Main conclusion: In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant's resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding.

NRC immune receptor networks show diversified hierarchical genetic architecture across plant lineages

“…TNLs and NRG1, along with their associated signalling partner SAG101, have been lost in monocots, some dicots, and some Magnoliids (Tarr and Alexander 2009; Collier et al 2011; Shao et al 2016; Liu et al 2021; Wu et al 2021). However, TNL and RNL are more highly expanded and diversified in Gymnosperms and Rosids (Terefe-Ayana et al 2012; Shao et al 2016; Van De Weyer et al 2019; Van Ghelder et al 2019; Woudstra et al 2023). CNLs are in general more abundant in the genomes of most angiosperms, whereas TNLs have been lost frequently in dicots (Liu et al 2021).…”