Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

Abstract

The concept of U’s triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2–6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U’s triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.

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

“…Genotyping by using six chloroplast SSR primer pairs or TILLING analysis, one most prevalent cpDNA haplotype was identified in B. napus [15,16]. 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]. A few B. napus accessions were grouped with the majority of B.…”

“…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]. Nap mitotype is predominant in natural B. napus,…”

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

“…Genotyping by using six chloroplast SSR primer pairs or TILLING analysis, one most prevalent cpDNA haplotype was identi ed in B. napus [15,16]. 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.…”

“…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]. The nap mitotype was further judged to be derived from B. oleracea, since it was phylogenetically grouped with botrytis-type and capitata-type B. oleracea [20].…”

The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity

“…Chloroplast genome comparison between Korea and China L. japonica collections revealed that the Korea collection was 18 bp shorter than China collection, 5 bp and 19 bp shorter in LSC and SSC regions, respectively, but 3 bp longer in each IR region. We identified 48 SNPs and 45 InDels between these two L. japonica collections that show richer intra-species diversity such as Panax ginseng and Brassica species (Kim et al 2015b(Kim et al , 2018Joh et al 2017;Nguyen et al 2017Nguyen et al , 2018.…”