Data from: Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Background: There are three basic Brassica genomes (A, B, and C) and three
parallel sets of subgenomes distinguished in the diploid Brassica (i.e.:
B. rapa, ArAr; B. nigra, BniBni; B. oleracea, CoCo) and the derived
allotetraploid species (i.e.: B. juncea, AjAjBjBj; B. napus, AnAnCnCn; B.
carinata, BcBcCcCc). To understand subgenome differentiation in B. juncea
in comparison to other A genome-carrying Brassica species (B. rapa and B.
napus), we constructed a dense genetic linkage map of B. juncea, and
conducted population genetic analysis on diverse lines of the three
A-genome carrying Brassica species using a genotyping-by-sequencing
approach (DArT-seq). Results: A dense genetic linkage map of B. juncea was
constructed using an F2 population derived from Sichuan Yellow/Purple
Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and
covered 1579 cM with an average density of two markers per cM. Based on
this map and the alignment of the marker sequences with the physical
genome of Arabidopsis thaliana, we observed strong co-linearity of the
ancestral blocks among the different A subgenomes but also considerable
block variation. Comparative analyses at the level of genome sequences of
B. rapa and B. napus, and marker sequence anchored on the genetic map of
B. juncea, revealed a total of 30 potential inversion events across large
segments and 20 potential translocation events among the three A
subgenomes. Population genetic analysis on 26 accessions of the three A
genome-carrying Brassica species showed that the highest genetic distance
were estimated when comparing Aj-An than between An-Ar and Aj-Ar subgenome
pairs. Conclusions: The development of the dense genetic linkage map of B.
juncea with informative DArT-seq marker sequences and availability of the
reference sequences of the Ar, and AnCn genomes allowed us to compare the
A subgenome structure of B. juncea (Aj) . Our results suggest that strong
co-linearity exists among the three A Brassica genomes (Ar, An and Aj) but
with apparent subgenomic variation. Population genetic analysis on three
A-genome carrying Brassica species support the idea that B. juncea has
distinct genomic diversity, and/or evolved from a different A genome
progenitor of B. napus.