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

Abstract

Background: The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and certain detailed interspecific relationships within Brassica genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions. Results: The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of Brassica materials, which contain 72 accessions and maximally integrated the known Brassica species. The Brassica genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around Brassica genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from B. juncea and B. carinata, the natural B. napus contains three major cytoplasmic haplotypes: the cam-type which directly inherited from B. rapa, polima-type which is close to cam-type as a sister, and the mysterious but predominant nap-type. Certain sparse C-genome wild species might have primarily contributed the nap-type cytoplasm and the corresponding C subgenome to B. napus, implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the B. napus cytoplasmic male sterile lines (e.g., mori and nsa). The genera Raphanus, Sinapis, Eruca, Moricandia show a strong parallel evolutional relationships with Brassica. Conclusions: The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of Brassica, which can substantially facilitate the development of novel Brassica germplasms.

De novo SNP calling reveals the genetic differentiation and morphological divergence in genus Amaranthus

“…For example, the genus Brassica comprises vegetable crops, such as cabbage ( Brassica oleracea L.) or oil crops, such as turnip ( B. rapa L.), which also includes vegetable crops such as bok‐choy [ B. rapa L. subsp. chinensis (L.) Hansel] (Cheng et al., 2016; Lin et al., 2014; Qiao et al., 2020). In this study, we propose that the use of amaranth for different purposes may result from the phenotypic divergence among different species given that amaranth is an ancient crop and has been consumed in various ways in different regions.…”

De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

“…Phenotype-driven utilization of a crop genus or species for different purposes is common in plants. For example, the genus Brassica comprises vegetable crops, such as Brassica oleracea , or oil crops, such as Brassica rapa , which also includes vegetable crops such as turnip and bok choy (Cheng et al, 2016; Lin et al, 2014; Qiao et al, 2020). In this study, we propose that the utilization of amaranths for different purposes may result from the phenotypic divergence among different species, given that amaranth is an ancient crop and has been consumed in various ways in different regions.…”

The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars (Brassica napus L.)

“…These Brassica reference genomes were sequenced and assembled long-read sequencing technologies using SMRT and Oxford Nanopore Technologies (MinION and higher throughput version of the MinION, PromethION) complemented with Illumina data and verified by optical mapping and/or Hi-C data [ 52 , 56 , 57 , 58 ]. Qiao et al [ 59 ] have proven cytoplasmic genomes from mitochondria and cytoplasms would be a highly effective approach for phylogenetic and evolutionary studies on B. napus including employing this resource in improved breeding.…”