Genome Triplication Drove the Diversification of Brassica Plants

Abstract

The genus Brassica belongs to the plant family Brassicaceae, which includes many important crop species that are used as oilseed, condiments, or vegetables throughout the world. Brassica plants comprise many diverse species, and each species contains rich morphotypes showing extreme traits. Brassica species experienced an extra whole genome triplication (WGT) event compared with the model plant Arabidopsis thaliana. Whole genome sequencing of the Brassica species Brassica rapa, Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants. Comparative genomic analysis based on the genome sequences of B. rapa and A. thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype (tPCK, n57) was the diploid ancestor of the three subgenomes in B. rapa. Following WGT, subsequent extensive genome fractionation, block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species. Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation. The subgenome dominance effect and biased gene retention, such as the over-retention of auxin-related genes after WGT, promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species. In conclusion, the WGT event initiated subsequent genomic and gene-level evolution, which further drove Brassica speciation and created rich morphotypes in each species. GENUS BRASSICA IN BRASSICACEAE Plants of the genus Brassica are grouped into the tribe Brassiceae, which belongs to the plant family Brassicaceae. Brassicaceae comprises a large family of plants that exhibit common and distinct features in their flowers. The flowers have cruciform petals and six stamens, two of which are short outer stamens. In total, Brassicaceae is composed of 3709 species and 338 genera, 1 with 308 of the 338 genera further assigned to 44 tribes.2 Among the abundant Brassicaceae species, the genus Brassica is important because it contains many economically valuable crops that are used as oilseeds, condiments, and culinary vegetables. Brassica species share an additional common feature in that they all experienced an extra whole genome triplication (WGT) event, which occurred approximately 9-15 million years ago 3,4 or even approximately 28 million years ago. 5-7THE U'S TRIANGLE MODEL DESCRIBES THE RELATIONSHIP AMONG BRASSICA CROPS Six species of the genus Brassica are used widely throughout the world as oilseed, condiments, fodder or vegetable crops. Three of these species are diploid (Brassica rapa, n510; B. nigra, n58; and B. oleracea, n59), whereas the other three are allotetraploids (B. juncea, n518; B. napus, n519; B. carinata, n517) derived from each pair of the three diploid species. The genetic relationships of these species were identified and confirmed by extensive experi...

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

“…Among several caleosin paralogs in Brassica plants, genes with higher expression levels are likely to play more important roles (Cheng et al 2014). Thus, BrCLO3-3, BrCLO4-2, BoCLO3-2, BoCLO4-1, BnCLO1-2, BnCLO1-3, BnCLO3-3 and BnCLO3-4 are worthy of further research, while the extremely low expression levels of BrCLO2-1, BrCLO2-2, BrCLO5, BnCLO2-1, BnCLO3-1, BnCLO4-5, BnCLO5-1, BnCLO5-2, and BnCLO8-3 might indicate that under normal growth conditions, they may play roles of less importance.…”

Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes

“…Repeat Evolution in Brassica AA, CC, and AACC Genomes • 111 Chalhoub et al (2014) 2015c). Eventually, independent rounds of genome reorganizations resulted in different chromosome numbers, genome sizes, genes and RE content, and gene retention and expression in different diploid Brassica species (Wang et al 2011b;Chalhoub et al 2014;Liu et al 2014;Cheng et al 2015b). Finally, recurrent merging of the AA and CC genomes occurred fewer than 1.0 million years ago, resulting in the allotetraploid AACC genome (Mun et al 2009;Chalhoub et al 2014).…”

“…Like most extant angiosperm species, the Brassica AA, CC, and AACC genomes have undergone numerous cycles of genome expansion and contraction through segmental or WGDs, followed by genome downsizing (Bowers et al 2003;Yang et al 2006;Barker et al 2009). These cycles are stimulated by environmental stresses, natural hybridization, or artificial selection (Kalendar et al 2000;Fedoroff 2012;Cheng et al 2015b). Often, large DNA segments -even whole chromosomes -are lost during this process (Koo and Jiang 2008).…”

“…In this process, a diploid ancestral genome with seven chromosomes, known as translocation Proto-Calepineae Karyotype (tPCK), likely hybridized via an allopolyploidization event to form a tetraploid with subgenomes, referred to as medium fractionated (MF1) and most fractionated (MF2) Tang et al 2012;Cheng et al 2015a). This was followed by another allopolyploidization with another diploid tPCK genome, least fractionated (LF), resulting in a genome with three sets of tPCK subgenomes, each with different levels of fractionation and reflecting different evolutionary timescales (Cheng et al 2015a;2015b; Repeats were estimated based on the reference mapping of major Brassica repeats from B. rapa (Waminal et al 2015), B. oleracea (Waminal et al 2016a), and B. napus (Waminal et al 2016b) to 1× WGS coverage.…”

“…actively involved in shaping these genomes. In fact, they play roles in the formation of subgenome dominance in B. rapa (Cheng et al 2015b) and are central to the epigenetic mechanisms that maintain cellular homeostasis (Fedoroff 2012). Despite their importance, REs are often responsible for bottlenecks in the genome assembly of short wholegenome sequence (WGS) reads.…”