The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Abstract

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. B. carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome-scale 1.31 Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

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

“…Insertion time of most LTRs ( B. rapa : 91.70%, B. nigra : 78.23%, R. sativus : 94.13%, S. alba : 89.61%, S. arvensis : 81.52%) in these five genomes was within 1 Mya. This indicates that these five species have experienced more recent expansion of retrotransposons than B. oleracea , which is consistent with a recent analysis comparing the Brassica B and C genomes (Yim et al., 2022). Within the LTR phylogenetic tree, composed of Ty1/Copia (6285) and Ty3/Gypsy (6398) superfamilies in B. rapa , B. nigra , S. alba , and S. arvensis , some species‐specific LTRs are observed, although there is no clear pattern to distinguish each of the four species (Figure S7).…”

Systematic analysis of MADS-box gene family in the U’s triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus

“…The B. carinata reference genome was published in 2021, marking the start of functional genomics. It also promoted the exploration of genetic evolution and molecular design breeding in the U’s triangle species ( Song et al., 2021 ; Yim et al., 2022 ). The MADS-box gene family is an important transcription factor that functions in floral homeostasis, morphogenesis, angiosperm reproductive development, and vegetative development ( Okada and Shimura, 1994 ; Becker et al., 2000 ; Alvarez-Buylla et al., 2019 ).…”

“…As an important oil crop in the world, B. napus was sequenced in 2014 ( Chalhoub et al., 2014 ), and many genome versions have been published ( Sun et al., 2017 ; Song et al., 2020 ; Chen et al., 2021 ), including the winter-type oilseed rape Darmor-bzh, semi-winter oilseed rape Zhongshuang11 (ZS11), and spring-type oilseed rape Westar and so on. Subsequently, the reference genomes of B. juncea ( Yang et al., 2016 ; Paritosh et al., 2021 ) and B. nigra were published successively ( Paritosh et al., 2020 ; Perumal et al., 2020 ), and the reference genome of B. carinata was the latest to be reported ( Song et al., 2021 ; Yim et al., 2022 ). To date, each of the six U’s triangle species has its reference genomes.…”

A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

“…The differences in the HC20 and zd-1 assembly could result from two possibilities: 1) the HC20 and zd-1 genomes may have arisen from distinct hybridization events; 2) the differences may be reconciled to the genome assembly artifacts. During the writing of our results, another chromosome-scale assembly of B. carinata line Gomenzer was published (Yim et al ., 2022). This assembly is closer in the quality metrics to the HC20 genome assembly (BUSCOs: zd-1 – 91.6%, Gomenzer – 97%, HC20 – 99.5%; LAI: zd-1 – 9.57, Gomenzer – 12.23, HC20 – 16.31).…”