Pangenomic origins of evolutionary rescue in a staple crop

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.
, , # 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 RMES...,