Data from: Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example

High-density linkage maps are important tools for genome biology and
evolutionary genetics by quantifying the extent of recombination, linkage
disequilibrium and chromosomal rearrangements across chromosomes, sexes
and populations. They provide one of the best ways to validate and refine
de novo genome assemblies, with the power to identify errors in assemblies
increasing with marker density. However, assembly of high-density linkage
maps is still challenging due to software limitations. We describe
Lep-MAP2, a software for ultra-dense genome-wide linkage map construction.
Lep-MAP2 can handle various family structures and can account for
achiasmatic meiosis to gain linkage map accuracy. Simulations show that
Lep-MAP2 outperforms other available mapping software both in
computational efficiency and accuracy. When applied to two large
F2-generation recombinant crosses between two nine-spined stickleback
(Pungitius pungitius) populations, it produced two high-density (~6
markers/cM) linkage maps containing 18 691 and 20 054 SNPs. The two maps
showed a high degree of synteny, but female maps were 1.5 to 2 times
longer than male maps in all linkage groups, suggesting genome-wide
recombination suppression in males. Comparison with the genome sequence of
the three-spined stickleback (Gasterosteus aculeatus) revealed a high
degree of interspecific synteny with a low frequency (<5%) of
interchromosomal re-arrangements. However, a fairly large (ca. 10Mb)
translocation from autosome to sex chromosome was detected in both maps.
These results illustrate the utility and novel features of Lep-MAP2 in
assembling high-density linkage maps, and their usefulness in revealing
evolutionarily interesting properties of genomes, such as strong
genome-wide sex-bias in recombination rates.