ABSTRACT Yellow monkeyflowers (Mimulus guttatuscomplex, 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 singleM. guttatuspopulation, one from the closely related selfing speciesM. nasutus, and one from a more divergent speciesM. 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, thisMimuluspan‐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 singleM. guttatuspopulation, ~7% within the interfertileM. guttatusspecies complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolatedM. tilingii. Genome‐wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high‐recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation forMimulusresearch and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.
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Genomics of Caddisfly (Insecta: Trichoptera) Species Associated With Terrestrial Habitats
ABSTRACT Limnephilidae is a species‐rich and ecologically diverse family within the tube case making clade of caddisflies (Trichoptera). Species occur across a wide range of habitats, from cold headwater streams to stagnant pools to terrestrial environments. Here, we sequenced, assembled, and annotated whole genomes from two species that are associated with terrestrial environments:Enoicyla pusilla(Burmeister, 1839), distributed in the West Palearctic, andPhilocasca rivularis(Wiggins, 1968), distributed in the Nearctic. Comprising three species,Enoicylais the only genus of Trichoptera in Europe that exhibits a completely terrestrial life‐cycle. As one of four species ofPhilocasca, larvae ofP. rivularisalso exhibit terrestrial behavior during wet months, dispersing across the forest floor up to several meters away from the stream channel. In both species, we investigated genomic features, for example, genome size and dynamics of transposable elements across Limnephilidae. We also explored potential molecular adaptations of silk to terrestrial versus aquatic environments. Characterization of the major silk gene,h‐fibroin, of both species, as well as elemental analysis of silk ofPhilocasca rivularis, did not reveal molecular differences compared with silk of aquatic caddisfly species, potentially owing to the humid environments that both species inhabit. The new genomes form key resources for future genomic research on insect evolution, particularly related to habitat diversification and aquatic‐terrestrial transitions.
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- Award ID(s):
- 2217155
- PAR ID:
- 10682011
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 16
- Issue:
- 4
- ISSN:
- 2045-7758
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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