DOI: 10.5061/dryad.56986
title: Data from: Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: 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.
description: Fig 4A
 markersThis data set contains
 16077 markers which was aligned to unique positions of A, B and C genomes
 (ABC-markers), respectively, and was used to construct the phylogenetic
 tree in Figure 4AFig4B
 markersThis data set contains
 3296 A genome specific markers of three A-genome containing species, and
 was used to construct the phylogenetic tree in Figure
 4BFig. 4 Phylogenetic tree
 of the three A genome contained species B. rapa, B. juncea and B.
 napusFigure 4 Phylogenetic
 tree of the three A genome contained species B. rapa, B. juncea and B.
 napus (A) Evaluated with a set of markers (16,077) which was aligned to
 unique positions of A, B and C genomes (ABC-markers), respectively; the
 figure shown B. juncea being separated from other two species. (B),
 Evaluated with a subset of markers (3,296) which were uniquely aligned to
 A genome; the figure shown a close relationship between B. juncea and B.
 rapa, and together separated from B. napus. 26 accessions of the three
 Brassica species, i.e, B. rapa, B. juncea and B. napus, were
 used.Genotype that used for
 Additional file 5Genotype that used for
 Additional file 6.xlsxAdditional File 5
 Phylogenetic tree of the three A genome-contained species evaluated with
 different sets of markersAdditional file 5
 Phylogenetic tree of the three A genome-contained species evaluated with
 different sets of markers. A, Evaluated with all of high-quality markers
 with genome alignments (28,267) (left), with a set of markers (16,077)
 which was aligned to unique positions of A, B and C genomes (ABC-markers,
 middle), and markers (12,781) which were uniquely aligned to B (8,278) and
 C (4,503) genomes(right), respectively. All of the three figures shown
 that B. juncea was separated from other two species. B, Evaluated with
 markers aligned to A genome uniquely (3,296) (left), and 3,296 A genome
 specific markers plus 11,321 markers with alignment on A genome along with
 positions on other genome(s). B. juncea and B. rapa shown close
 relationship and separated from B. napus.Information of
 DArT-SeqTM markers and genotypes of the 26 diverse lines from the three A
 genome-carrying speciesInformaetion of
 DArT-SeqTM markers and genotypes of the 26 diverse lines from the three A
 genome-carrying species and the aligment of the 47550 marker sequences to
 the genome of the three A genome-carrying species