DOI: 10.5061/dryad.q018v
title: Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing

description: Marine populations of the threespine stickleback (Gasterosteus aculeatus)
 have repeatedly colonized and rapidly adapted to freshwater habitats,
 providing a powerful system to map the genetic architecture of evolved
 traits. Here, we developed and applied a binned genotyping-by-sequencing
 (GBS) method to build dense genome-wide linkage maps of sticklebacks using
 two large marine by freshwater F2 crosses of more than 350 fish each. The
 resulting linkage maps significantly improve the genome assembly by
 anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and
 rearranging scaffolds in 4 locations. In the revised genome assembly,
 94.6% of the assembly was anchored to a chromosome. To assess linkage map
 quality, we mapped quantitative trait loci (QTL) controlling lateral plate
 number, which mapped as expected to a 200-kb genomic region containing
 Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously
 identified modifier QTL. Finally, we mapped eight QTL controlling
 convergently evolved reductions in gill raker length in the two crosses,
 which revealed that this classic adaptive trait has a surprisingly modular
 and nonparallel genetic basis.
description: READMESummary of all files in
 this Dryad packageFileS4
 NewScaffoldOrder.csvRevised scaffold order
 for each chromosome (consensus of FTC and BEPA). Revised coordinates
 (based on this study) and original assembly coordinates are presented.
 Orientations are defined relative to original genome assembly. The
 orientation of some scaffolds was not detected in this study. These
 scaffolds are labeled as having 'unknown' orientation; their
 orientation was not altered relative to their orientation in the original
 genome assembly. Chromosome 'M' is the mitochondrial genome
 sequence, which was not analyzed in this study but is replicated in the
 revised genome assembly.FileS5
 revisedAssemblyUnmasked.fa.zipFasta file containing
 revised genome assembly based on consensus scaffold order and orientation
 as described in File S4 in the Glazer et al. manuscript. File is
 zipped.FileS6
 revisedAssemblyMasked.fa.zipRepeat masked fasta file
 containing revised genome assembly based on consensus scaffold order and
 orientation as described in File S4 in the Glazer et al. manuscript.
 Repeat masked fasta file is based off the repeat masked version of the
 original genome assembly, which was masked with RepeatMasker. File is
 zipped.FileS7
 ensGene_revised.gtfRevised .gtf file of
 Ensembl gene predictions. Coordinates of gene predictions were converted
 to the revised assembly coordinates. All Ensembl-predicted genes were
 included, except ENSGACT00000019430, which spans two scaffolds (11 and 79)
 that are not adjacent in the revised genome assembly. File is
 zipped.ScafKeyForNewFasta.csvKey for scaffold order in fasta filesSampleList.csvList of all samples and barcodes in the GBS F2s.convertCoordinate.RThis R function converts between the 'old' and 'new' stickleback assembly coordinate systems. The 'old' coordinate system is the assembly described in the Jones et al 2012 stickleback genome paper. It requires access to the FileS4 NewScaffoldOrder.csv file. It has 4 inputs: chr, pos, direction, and scafFile. It returns a list of [chromosome, position]. See README or comments in convertCoordinate.R for further details.