DOI: 10.5061/dryad.qz612jmv9
title: Pangenomic origins of evolutionary rescue in a staple crop

description: 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.
description: # Pangenomic origins of evolutionary rescue in a staple crop Dataset DOI:
 [10.5061/dryad.qz612jmv9](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](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: * [https://github.com/CropAdaptationLab/RMES1genefamily](https://github.com/CropAdaptationLab/RMES1genefamily)