Genomic diversity and evolution of seven Brassica species revealed by whole genome resequencing

Abstract

The Brassica genus contains the most diverse collection of agronomically important plant species and is a relative of the model plant Arabidopsis thaliana, from which it diverged ~20 MYA. The six most agro-economically important Brassica species include the three diploid species, Brassica rapa (AA, 2n = 20), Brassica oleracea (CC, 2n = 18), and Brassica nigra (BB, 2n = 16)

and the three allotetraploid species, Brassica juncea (AABB, 2n = 34), Brassica napus (AACC, 2n = 38), and Brasscia carinata (BBCC, 2n = 36), which were formed through the hybridization of their diploid genome counterparts. To understand genetic relationship and evolution of the Us triangle in Brassica species, whole genome resequencing of 28 Brassica species belonging to A, B, C, R, AB, AC, and BC genome was conducted using Illumina MiSeq next-generation sequencing platform. Approximately 6~8 million sequence reads were obtained from each genotype and ~80% of them were high quality sequences. Overall, ~87% of the total pre-processed sequence reads from each genotype were mapped to publicly available multiple reference genomes including A. thaliana, B. rapa, B. oleracea, and B. napus. The average mapping depth was over three-fold for each genotype, and 59 million high-confidence genome-wide single-nucleotide polymorphisms (SNPs) and 247,407 indels were detected across the reference genomes. Using Arabidopsis as a reference, variants derived from exon were much higher than that of from intergenic or intron, which suggested that intergenic and intron sequences went divergent faster after Arabidopsis and Brassica species split. In comparison of all four kinship analysis based on SNPs with multiple references (A. thaliana, B. rapa, B. oleracea and B. napus), each of the four accessions representing a diploid genome type was grouped in a cluster regardless of reference genome. The position of allotetraploid genomes in phylogenic tree was incongruent due to the complex history of Brassica lineage when multiple Brassica references were used, however the genetic relationship including allotetraploid wasmore clearly explained with higher quality SNPs using A. thaliana as a reference. In order to reveal the diversity, origin and evolution of Brassica species, additionally a comprehensive phylogenetic analysis of 28 Brassica species was carried out based on complete chloroplast (CpDNA) and 45S ribosomal sequences (nrDNA). Concurrent phylogenomic analysis elucidates the genetic diversity, relationship, maternal source for allotetraploids and evolution of the Brassica species. In addition, complete map of the structural variants such as SNPs, indels, and copy number variations for CpDNA and nrDNA were constructed. An independent estimation of divergence time, based on CpDNA and nrDNA together with previous reports reveals the allotetraploids were diverged about 0.01 MYA. Structural variants such as SNP and indel have provided potential barcoding markers for identification of each Brassica species including Raphanus sativus. Certainly, the use of CpDNA and nrDNA provides a comprehensive overview of the genome diversity and evolutionary context of the major Brassica species.