Pangenomic origins of evolutionary rescue in a staple crop
Data files
Sep 25, 2025 version files 549.11 KB
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Fig_4f_-_RMES1_canonical_NLRs.aln.fasta
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Fig_5b_-_RMES1_poaceae_gene_family.aln.fasta
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Fig_5b_-_RMES1_poaceae_gene_family.tre
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Fig_5c_-_RMES1_NB-domain_uniprot_gene_family.aln.fasta
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Fig_5c_-_RMES1_NB-domain_uniprot_gene_family.tre
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Fig_S9_-_RMES1_sorgpan_gene_family.aln.fasta
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Fig_S9_-_RMES1_sorgpan_gene_family.tre
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README.md
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Abstract
This repository includes multiple sequence alignments and phylogenetic trees of RMES1-like genes in the sorghum pangenome and across Poaceae. The recent adaptation of the cereal crop sorghum to a global aphid outbreak was a fortuitous case of evolutionary rescue, but the pangenomic and molecular basis is not known. The sorghum pangenome contains extensive copy number variation at the locus and a segmental duplication on Chr10 (Fig. S9). The causative NLRs (RMES1A and RMES1B) lack signaling domains and have ATPase mutations expected to abrogate function (Fig. 4f), suggesting RMES1 NLRs regulate immunity via a noncanonical mechanism. The RMES1 NLR family is ancient, orthologous to phloem-feeding resistance genes in rice (Fig 5b) and syntenic across the grass super-pangenome (Fig. 5b, 5c). Thus, gene birth-and-death processes at an ancient gene cluster created rare standing variation and provided the adaptive allele for evolutionary rescue.
Dataset DOI: 10.5061/dryad.qz612jmv9
Description of the data and file structure
Multiple sequence alignments and the associated phylogenetic trees (Fig. 4f MSA was not used for phylogenetic tree) are included here for the publication "Ancient pangenomic origins of noncanonical NLR genes underlying the recent evolutionary rescue of a staple crop" (https://doi.org/10.1101/2025.04.11.648396).
The sorghum pangenome reveals substantial copy number variation at this locus, including a segmental duplication on chromosome 10 (Fig. S9). The key NLR genes involved, RMES1A and RMES1B, lack typical signaling domains and carry ATPase domain mutations that are predicted to disrupt their function (Fig. 4f). This suggests that RMES1 NLRs may mediate immune responses through a noncanonical mechanism. Phylogenetic and synteny analyses indicate that the RMES1 NLR family is ancient, orthologous to known resistance genes against phloem-feeding pests in rice (Fig. 5b), and conserved across the grass super-pangenome (Fig. 5b, 5c). These findings support the idea that gene birth-and-death dynamics at this long-standing gene cluster have generated rare standing variation, ultimately giving rise to an adaptive allele that enabled evolutionary rescue.
Files and variables
File: Fig_4f_-_RMES1_canonical_NLRs.aln.fasta
Description: Alignment of RMES1 genes with canonical NLRs
File: Fig_S9_-_RMES1_sorgpan_gene_family.tre
Description: Phylogenetic tree of RMES1 homologs in the sorghum pangenome
File: Fig_5b_-_RMES1_poaceae_gene_family.tre
Description: Phylogenetic tree of RMES1 homologs in Poaceae representatives
File: Fig_S9_-_RMES1_sorgpan_gene_family.aln.fasta
Description: Alignment of RMES1 homologs in the sorghum pangenome
File: Fig_5c_-_RMES1_NB-domain_uniprot_gene_family.tre
Description: Phylogenetic tree of RMES1 homologs in the Ref90 database
File: Fig_5b_-_RMES1_poaceae_gene_family.aln.fasta
Description: Alignment of RMES1 homologs in Poaceae representatives
File: Fig_5c_-_RMES1_NB-domain_uniprot_gene_family.aln.fasta
Description: Alignment of RMES1 homologs in the Ref90 database
Access information
Other publicly accessible locations of the data: