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

Abstract

Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, Chinese kale originated in southern China. The chloroplast genome is often used for phylogenetic analysis because of its high conservatism. Fifteen pairs of universal primers were used to amplify the chloroplast genomes of white-flower Chinese kale (Brassica oleracea var. alboglabra cv. Sijicutiao (SJCT)) and yellow-flower Chinese kale (Brassica oleracea var. alboglabra cv. Fuzhouhuanghua (FZHH)) via PCR. The lengths of the chloroplast genomes were 153,365 bp (SJCT) and 153,420 bp (FZHH) and both contained 87 protein-coding genes and eight rRNA genes. There were 36 tRNA genes in SJCT and 35 tRNA genes in FZHH. The chloroplast genomes of both Chinese kale varieties, along with eight other Brassicaceae, were analyzed. Simple sequence repeats, long repeats, and variable regions of DNA barcodes were identified. An analysis of inverted repeat boundaries, relative synonymous codon usage, and synteny revealed high similarity among the ten species, albeit the slight differences that were observed. The Ka/Ks ratios and phylogenetic analysis suggest that Chinese kale is a variant of B. oleracea. The phylogenetic tree shows that both Chinese kale varieties and B. oleracea var. oleracea were clustered in a single group. The results of this study suggest that white and yellow flower Chinese kale comprise a monophyletic group and that their differences in flower color arose late in the process of artificial cultivation. Our results also provide data that will aid future research on genetics, evolution, and germplasm resources of Brassicaceae.

Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi (Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea

“…These Eutrema hotspot regions can be compared to those of other Brassicaceae congeneric species. For the six species of Triangle U Brassica species and closely related two Sinapis species (Brassicaceae), five mutation hotspots were identified for DNA barcoding markers and phylogenetic analysis: psbA, matK/rps16, rpl32, rpl32/trnL, and ycf1 [38]. For the six species of Orychophragmus in Brassicaceae [39], nine intergenic spacers were identified as divergence hotspots: trnH/psbA, atpI/rps2, trnM/atpE, atpB/rbcL, ndhC/trnV, accD/PsaI, petB/petD, rpl23/trnL, and ndhE/ndhG.…”

Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Kohlrabi (Brassica oleracea var. gongylodes L.)

“…Four forms of interspersed repeat sequences were identified: forward, palindromic, reverse and complementary repeat sequences. The SSRs were identified using MISA v1.0 (MIcroSAtellite identification tool, http://pgrc.ipk-gatersleben.de/misa/misa.html, accessed on 23 March 2023) software, in which parameters were set as single-base repeat > 8, di-base repeat > 5, tri-base repeat > 3, tetra-base repeat > 3, penta-base repeat > 3, and hexa-base repeat > 3 [15,39,40]. The SSR primers were designed using the SSR analysis results.…”

“…The cp genome is a maternally inherited genetic systems of plants, which is not affected by karyogene deletion, overlap, or pseudogenes [15]. In the cp genome, a large number processes, such as regulation of plant physiology, growth, development, and stress responses [12][13][14].…”

“…The cp genome is a maternally inherited genetic systems of plants, which is not affected by karyogene deletion, overlap, or pseudogenes [15]. In the cp genome, a large number of mutational events also occur, such as nucleotide substitutions, insertions, deletions, and genome fragment inversions, translocations and rearrangements [16][17][18].…”

“…In the cp genome, a large number of mutational events also occur, such as nucleotide substitutions, insertions, deletions, and genome fragment inversions, translocations and rearrangements [16][17][18]. In most angiosperms, chloroplasts have a typical quadripartite circular genome, which comprises one large single-copy (LSC) region with a length of about 81-90 kb, one small single-copy (SSC) region of approximately 18-20 kb, and two inverted repeat (IR) regions of about 20-30 kb, named IRa and IRa [13,15,19]. Oldenburg and Bendich [20] reported that a linear cp genome was found in maize.…”