Sinapis genomes provide insights into whole‐genome triplication and divergence patterns within tribe Brassiceae

Abstract

SUMMARY Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra, S. alba, and S. arvensis, and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole‐genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole‐genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba diverged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the divergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea. Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.

Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae

“…In Alliaria petiolata , the two FLC -like genes are more than 500 kbp apart but still on the same scaffold and probably originated from a segmental duplication. Camelina sativa, as well as the Brassiceae Brassica rapa , Sinapis alba , Moricandia moricandioides, and Crambe hispanica , experienced a whole genome triplication (WGT) in the lineages leading to them [ 53 , 54 ]. Consequently, all of these species hold three FLC -like genes s.str .…”

Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra)

“…B. carinata has been shown to be derived from interspecific hybridization between the diploid progenitors B. nigra and B. oleracea [ 18 , 19 ]. S. alba , also known as Brassica hirta , is a white-flowered or yellow-flowered annual plant in the family Brassicaceae [ 20 ]. Therefore, we included two Sinapis species in our comparative analysis in addition to the eight Brassica species.…”

Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

“…speltoides [ 46 ], Ae. tauschii [ 47 ], Avena insularis , A. sativa and A. longiglumis [ 30 ], A. atlantica and A. eriantha [ 48 ], H. vulgare MorexV3 [ 49 ] (the outgroup in the analysis of both wheats and oats), P. rhoeas (which served as the outgroup in the analysis of the following two poppy species), P. somniferum and P. setigerum [ 50 ], B. juncea [ 51 ], B. napus zs11 [ 52 ], B. carinata [ 53 ], B. oleracea [ 54 ], B. rapa [ 55 ], B. nigra and Sinapis alba [ 56 ] (the outgroup for the analysis of Brassica spp. ), F. × ananassa FL15.89–25 v1.0 [ 57 ], F. vesca v6.0 [ 23 ], F. iinumae [ 26 ], F. viridis [ 27 ], F. nipponica [ 58 ] and R. idaeus [ 59 ] (the outgroup for the analysis of the strawberries), were obtained from public databases or were provided by the corresponding authors, as detailed in Table S1 .…”