A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U

Abstract

The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions. Here, we successfully de novo assembled 60 complete chloroplast genomes of Brassica genotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of different Brassica species was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated the Brassica genus into four clades. B. carinata and B. juncea share their chloroplast genome with one of their hybridization donors B. nigra and B. rapa, respectively, which fits the U model. B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions. B. napus clearly has evidence for two independent hybridization events, as it contains either B. rapa chloroplast genomes. The divergence estimation suggests that B. nigra and B. carinata diverged from the main Brassica clade 13.7 million years ago (Mya), while B. rapa and B. oleracea diverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic relationships within the Brassica genus.

Synchronous dissection of chloroplast and mitochondrial genomes clarifies the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

“…rapa accessions suggested another independent cytoplasmic origin from B. rapa [9,18]. The mitochondrial DNA (mtDNA) of B. napus has drawn much more attention for the extensive application of its cytoplasmic male sterility (CMS) lines in hybrid breeding, mainly containing polima (pol), cam and nap mitotypes in the natural resources [17].…”

“…Brassica genus is proposed in Figure 6. Surprisingly, the B. rapa variety broccoletto had been previously identified possessing identical cpDNA haplotype as the nap-type B. napus [15,18].…”

“…The investigated broccoletto accession collected from Italy were generally cultivated alongside multifarious wild Brassica species [18]. Whereupon, the presence of nap-type haplotype in these B.…”

Characterization of the complete chloroplast genome sequence and phylogenetic analysis of B. oleracea var. italica

“…The cpDNA-based phylogenetic analysis has revealed better understanding of evolutionary relationship, population analysis and classification in rice species [25], Brassica genus [26], Myrtales species [27], and Aristolochia species [3]. To investigate the taxonomic status and evolutionary relationship of broccoli, alignment of 9 complete cp genomes downloaded from NCBI Gene Bank database was performed, and a ML tree was constructed by FastTree.…”

Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica

“…While, the B. napus of this same cpDNA haplotype generally formed an ambiguous clade, which did not group with the investigated B. rapa or B. oleracea accessions [17], implying its mysterious origin. A few B. napus accessions were grouped with the majority of B. rapa accessions suggested another independent cytoplasmic origin from B. rapa [9,18], indicating that has multiplex maternal origins. The mitochondrial DNA (mtDNA) of B. napus has drawn much more attention for the extensive application of its cytoplasmic male sterility (CMS) lines in the heterosis-driving hybrid breeding, mainly containing polima (pol), cam and nap mitotypes in the natural resources [17].Nap mitotype is predominant in natural B. napus, However, it remains unsolved and were supposed to be from an unidenti ed or lost mitotype of B. rapa [19].…”