Local adaptation and the evolution of genome architecture in threespine stickleback
Creators: name: Li, Qiushi
name: Lindtke, Dorothea
name: Rodríguez-Ramírez, Carlos
name: Kakioka, Ryo
name: Takahashi, Hiroshi
name: Toyoda, Atsushi
name: Kitano, Jun
name: Ehrlich, Rachel
name: Mell, Joshua
name: Yeaman, Sam
Publisher: name: Zenodo
Year: 2023
Subjects: Genomic Resources
threespine stickleback
tubesnout

description: Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a <em>de novo</em> assembly of the closely-related tubesnout (<em>Aulorhyncus flavidus</em>) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
description: Please contact samuel.yeaman@ucalgary.ca with any questions.Funding provided by: Natural Sciences and Engineering Research Council of Canada<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000038<br>Award Number: Funding provided by: Alberta Innovates<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100009192<br>Award Number: Funding provided by: Japan Society for the Promotion of Science<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691<br>Award Number:
description: This archive contains materials related to the paper "Local adaptation and the evolution of genome architecture in threespine stickleback", by Li et al. There are 3 main directories. The directory of genomic resources is on Dryad, the directories of scripts and supplemental information are on Zenodo. - Genomic_resources: the genome assemblies, annotations, and lists of genes - Supplemental information: contains the processed intermediate data files necessary to generate the figures and tables in the paper, as well as the Hi-C config files - scripts: contains the scripts for running the main analyses and generating the figures/tables