The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs

Abstract

The NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of the RNL subfamily and a lack of data in Gymnosperms. We developed, searched and annotated transcriptomes assemblies of seven conifers and identified a resource of 3816 expressed NLR sequences. Our analyses encompassed sequences data spanning the major groups of land plants and determinations of NLR transcripts levels in response to drought in white spruce. We showed that conifers have among the most diverse and numerous RNLs in tested land plants. We report an evolutionary swap in the formation of RNLs, which emerged from the fusion of an RPW8 domain to a NB-ARC domain of CNL. We uncovered a quantitative relationship between RNLs and TNLs across all land plants investigated, with an average ratio of 1:10. The conifer RNL repertoire harbours four distinct groups, with two that differ from Angiosperms, one of which contained several upregulated sequences in response to drought while the majority of responsive NLRs are downregulated.

A Reference Genome Sequence for Giant Sequoia

“…Of the 984, 712 included intact NB-ARC domains with fewer than 50% gaps in the alignment. This number is roughly twice the number of NLR genes found in cultivated rice (Zhou et al 2004;Read et al 2020) and is consistent with other conifers (Van Ghelder et al 2019). NLR-gene coordinates of all NLR gene sequences in giant sequioa 2.0, and the relationships of the 712 based on an NB-ARC domain maximum likelihood tree are included in Supplementary Table S8, S9, and S10 as well as Supplementary Figure S3.…”

“…In crop species, NLR genes also have demonstrated contributions to resistance against insects (Stahl et al 2018). A recent examination of transcriptome data from several conifer species showed that many conifer NLR genes are downregulated in response to drought (Van Ghelder et al 2019), suggesting contrasting roles in biotic versus abiotic stress responses. Cataloging NLR genes in giant sequoia is a step toward understanding their impact in relation to conservation and management.…”

The giant sequoia genome and proliferation of disease resistance genes

“…NLR-gene coordinates of all NLR gene sequences, and the relationships of the 712 based on an NB-ARC domain maximum likelihood tree are included in Supplementary Table S5, S6, and S7 as well as Supplementary Figure S1. This number is roughly twice the number found in (Zhou et al, 2004;Read et al, 2020) and is consistent with other conifers (Van Ghelder et al, 2019).…”

“…Determination of TIR and CC domains was based on motif data from Jupe and colleagues (2012). RPW8-like motifs were determined by alignment to a recently described RNL motif (CFLDLGxFP) (Van Ghelder et al, 2019).…”

“…In plants, disease resistance is typically conferred by genes encoding nucleotide binding leucine-rich repeat (NLR) proteins that individually mediate responses to different pathogens. In crop species, NLR genes have demonstrated contributions to resistance against insects (Stahl et al, 2018), and a recent examination of transcriptome data from several conifer species showed that many conifer NLRs were induced following drought stress (Van Ghelder et al, 2019), suggesting an even broader role. Their importance in resilience to disease and abiotic stress makes cataloging NLR genes of particular interest for conservation and management.…”