Deciphering the Diploid Ancestral Genome of the MesohexaploidBrassica rapa   

Abstract

The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers.

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…So far, the genomes of six crucifer species have been partially or completely sequenced, including those of (i) the model 8 9 2 VOLUME 45 | NUMBER 8 | AUGUST 2013 Nature GeNetics A r t i c l e s plant A. thaliana 24 ; (ii) Arabidopsis lyrata, a congener of A. thaliana with a more ancestral karyotype and genome size 25 ; (iii) Capsella rubella, which falls in the sister group to the genus Arabidopsis 26 ; (iv) Brassica rapa (Chinese cabbage 27 ), one of the several closely related Brassica crop species in the tribe Brassiceae that share a recent genome triplication event (Br-α) 28 ; (v) Eutrema salsugineum (previously Thellungiella halophila) of the tribe Eutremeae, an extremophile adapted to saline habitats 29 ; and (vi) Schrenkiella parvula (previously Thellungiella parvula) 30 , another extremophile of uncertain tribal placement.…”

“…Protein-coding genes and transposable elements (TEs) were predicted across all nine genomes ( This variation was expected given the rediploidization process following the At-α duplication and several whole-genome amplifications after At-α (for example, the Brassica triplication 28 ). TEs comprised the majority of the variation in genome size observed across the crucifers, varying in content from 13-15% in the smallest genomes (A. thaliana and S. parvula) to ~50% in E. salsugineum.…”

Genome Triplication Drove the Diversification of Brassica Plants

“…The breakage and formation of block associations occur independently; thus, the probability that an ancestral block association was broken more than twice after WGT is low, and the probability that a newly derived block association formed more than twice after WGT is also low. Based on this rule, by counting the copy numbers of all block associations in genome of B. rapa and comparing these numbers with the extant diploid karyotypes in Brassicaceae, such as ACK, PCK, tPCK and A. thaliana, Cheng and co-workers 24 found that the diploid ancestor of B. rapa had a tPCKlike karyotype. Furthermore, block association analysis of B. oleracea or B. napus and R. sativus based on genetic maps showed that these species also evolved from an ancestor having a tPCK genome.…”

Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis)

“…Chinese cabbage (Brassica rapa ssp pekinensis), an important vegetable crop originating from China, is considered to be a classic representative of the A genome of Brassica. The B. rapa genome is derived from the genome of a hexaploid ancestor, a triplicated diploid ancestral genome closely related to the A. thaliana genome (Wang et al, 2011;Cheng et al, 2013). The hexaploid ancestor of B. rapa is believed to have had three subgenomes, that have been designated on the basis of gene density and rate of gene loss (fractionation) as LF (the least fractionated), MF1 (the medium fractionated), and MF2 (the most fractionated) (Wang et al, 2011).…”

“…Brassica rapa may have had a two-step origin; the first step being tetraploidization, followed by substantial genome fractionation, thus producing MF1 and MF2 genomes. The tetraploidized genome then subsequently hybridized with a third, less-fractionated genome (LF) Tang et al, 2012;Cheng et al, 2013).…”