DOI: 10.5061/dryad.1c59zw3w3
title: Local adaptation and the evolution of genome architecture in threespine stickleback

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 de novo assembly
 of the closely-related tubesnout (Aulorhyncus flavidus) 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: 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
description: Please contact samuel.yeaman@ucalgary.ca with any questions.
description: This archive contains material related to the paper "Local adaptation
 and the evolution of genome architecture in threespine stickleback",
 by Li et al. GENERAL INFORMATION * Data (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 SHARING/ACCESS INFORMATION 1. Licenses/restrictions
 placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to
 publications that cite or use the data: Li Q, Lindtke D, Rodríguez-Ramírez
 C, et al. Local adaptation and the evolution of genome architecture in
 threespine stickleback. Genome Biology and Evolution. 2022,14(6): evac075.
 https://doi.org/10.1093/gbe/evac075 3. Recommended citation for this
 dataset: Li Q, Lindtke D, Rodríguez-Ramírez C, et al (2022). Data from:
 Local adaptation and the evolution of genome architecture in threespine
 stickleback. Dryad Digital Repository.
 https://doi.org/10.5061/dryad.1c59zw3w3
 #########################################################################
 LSGs\_permissive.txt: permissive filtered putative lineage-specific genes
 1. Variable List: ID: gene ID stick\_chrom: chromosome number in the
 stickleback genome stick\_start: start position on the chromosome
 stick\_end: end position of the chromosome 2. Specialized formats: None
 #########################################################################
 LSGs\_stringent.txt: stringent filtered lineage-specific genes 1. Variable
 List: ID: gene ID stick\_chrom: chromosome number in the stickleback
 genome stick\_start: start position on the chromosome stick\_end: end
 position of the chromosome 2. Specialized formats: None
 #########################################################################
 Peichel\_job\_3.hints.cds.reformat.uniq\_combined\_BROADS1.fasta:
 stickleback gene sequences 1. Variable List: None 2. Specialized formats:
 can be read by any text editor (TextEdit, Notepad, VIM, etc.)
 #########################################################################
 duplicates.txt: the ID and position of duplicated genes 1. Variable List:
 ID: gene ID stick\_chrom: chromosome number in the stickleback genome
 stick\_start: start position on the chromosome stick\_end: end position of
 the chromosome 2. Specialized formats: None
 #########################################################################
 microrearrangements.txt: the ID and position of micro-rearranged genes 1.
 Variable List: ID: gene ID stick\_chrom: chromosome number in the
 stickleback genome stick\_start: start position on the chromosome
 stick\_end: end position of the chromosome 2. Specialized formats: None
 #########################################################################
 stb\_stickleback\_gene\_full.gff3: stickleback gene mapping results 1.
 Variable List: None 2. Specialized formats: gff3, has 9 required fields of
 ID (chromosome number), Source, Feature, Start, End, Score, Strand, Phase,
 Artributes. Can be read by any text editor, or Genome Browsers like [IGV].
 #########################################################################
 tsnV2.2\_hints.cds.reformat.uniq.fasta: tubesnout gene sequences 1.
 Variable List: None 2. Specialized formats: can be read by any text editor
 (TextEdit, Notepad, VIM, etc.)
 #########################################################################
 tsnV2.2\_hints.gtf: de novo gene annotation of the tubesnout genome 1.
 Variable List: None 2. Specialized formats: gtf, has 9 required fields of
 ID (chromosome number), Source, Feature Type, Start, End, Score, Strand,
 Phase, Artributes. Can be read by any text editor, or Genome Browsers like
 [IGV].
 #########################################################################
 tubesnoutV2.2\_chr1-23\_and\_UN.fasta.gz: the assembled tubesnout genome
 1. Variable List: None 2. Specialized formats: this is a compressed fasta
 file. Unzip first, then it can be read by any text editor (TextEdit,
 Notepad, VIM, etc.) Please contact samuel.yeaman@ucalgary.ca with any
 questions.