The genome of the mesopolyploid crop species Brassica rapa

Abstract

The genome of the mesopolyploid crop species Brassica rapaThe Brassica rapa Genome Sequencing Project Consortium 1 Abstract:The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70%) than the remaining two (46% and 36%). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.2

A heterozygous moth genome provides insights into herbivory and detoxification

“…This is around the time of the divergence of mono-and dicotyledonous npg l e t t e r s plants (~304 million years ago) 15 , consistent with the coevolution and concurrent diversification of insect herbivores and their host plants. It can be predicted that P. xylostella became a cruciferous specialist when Cruciferae diverged from Caricaceae (~54-90 million years ago) 16 , which provides additional evidence to support our estimation of the divergence time (~124 million years ago) of P. xylostella from two other Lepidoptera, B. mori and D. plexippus (Fig. 2).…”

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

“…However, as heterozygosity is likely to occur in regions it may be possible to collate information from several adjacent SNPs to define a region of heterozygosity. complex, sharing a whole genome triplication (Liu et al, 2014;Parkin et al, 2014;Wang et al, 2011), and the assembly of the recent Brassica C genome is of greater quality than the A genome assembly which was published three years earlier . While the chickpea genome reference is not perfect this relatively simple genome, produced using the latest sequencing chemistry and assembly methods is likely to have fewer misassembled regions than the Brassica genomes.…”

“…For B. napus, two reference sequences relating to the B. napus diploid progenitors were used for mapping reads, the A-genome (Wang et al, 2011) and the C-genome . The Brassica population consisted of 92 double-haploid Tapidor X Ningyou 7 individuals from the TNDH mapping population previously described (Qiu et al, 2006) (see Supplementary Table 1 for a full overview).…”

“…Genomic information is becoming increasingly available for Brassica and chickpea species. Proprietary genome sequences for B. napus and its diploid progenitor species were produced in 2009 (http://www.brassicagenome.net/), a public B. rapa genome was published in 2011 (Wang et al, 2011), the genome of B. oleracea (CC) was published recently (Liu et al, 2014;Parkin et al, 2014), and the genome of B. napus (AACC) is expected to become available in the next 12 months. Draft references of both kabuli and desi chickpea genomes were also published in 2013 (Jain et al, 2013;Varshney et al, 2013b).…”

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…However, chromosome sorting is less useful for cotton, which has a large number of small chromosomes (2n = 4x = 52). A conventional approach is to sequence diploid progenitor genomes, which can then guide the assembly of homoeologous chromosomes of allopolyploids, as was done for Brassica napus [7][8][9] . One problem with this approach is that many sequence contigs and scaffolds remain ambiguous with respect to homoeologous relationships.…”