Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower ( Mimulus guttatus ) Complex

作者：John T. Lovell, Rachel Walstead, Amelia Lawrence, Evan Stark‐Dykema, Matthew C. Farnitano, Avril M. Harder, Tomáš Brůna, Kerrie Barry, David Goodstein, Jerry B. Jenkins, Anna Lipzen, LoriBeth Boston, Jenell Webber, Mansi Chovatia, Joanne Eichenberger, Jayson Talag, Jane Grimwood, Jeremy Schmutz, John K. Kelly, Andrea L. Sweigart, Lila Fishman, John H. Willis · 发表于：Molecular Ecology Resources · 年份：2025 · DOI：10.1111/1755-0998.70012 · 被引用次数：10 · 研究领域：Genetic diversity and population structure、Genetic and Environmental Crop Studies、Plant and animal studies

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked sele...