A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L

Abstract

Background: Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.

Results: Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.

Conclusions: The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.

Keywords: Brassica; Cytoplasm haplotype; Maternal ancestor; Mitotype; Organelle pan-genome; Rapeseed.

Fig. 1

Sequence feature of assembled chloroplast and mitochondrion genomes. A Length distribution of mitochondrial genomes and B chloroplast genomes. C G + C content of mitochondrial genomes and D chloroplast genomes

Fig. 2

Circular genome maps and distribution of variants of the A Chloroplast and B mitochondrial Genome of Brassica napus. The outer circle is the organellar genome map displaying genes in different functional categories (listed in the legend) distinguished by colors. Genes marked inside the circle are transcribed clockwise, while outside the circle are counter clockwise. The inner circle displays the distribution of variants in different groups, the dark gray bars representing all assembled accessions, and blue highlights corresponding to four different cytoplasm (nap, cam, pol and ole), the higher the bar or the darker the color, the greater the density. The length of each bar denotes the total number of variants in a 500-bp window

Fig. 3

Organelle genome- and subgenome-wide comparison of nucleotide diversity and FST during the four main cytoplasm ypes of B. napus. A Nucleotide diversity and Fst between four group based on cpDNA. B Nucleotide diversity and Fst between four group based on mtDNA. C Nucleotide diversity along cp genome except the two inverted repeat region. D Nucleotide diversity along mt genome. π values were estimated for 500-bp sliding windows with 100-bp step size along organellar genomes across different cytoplasmic groups

Fig. 4

Population structure of B. napus accessions and its two progenitor species. A PCA plot of assembled cp genomes. B Chloroplast phylogeny of assembled B. napus combined together with 199 B. rape, 119 B. oleoracea and 31 synthetic B. napus accessions. C Mitochondria phylogeny of B. napus and its two progenitor species. D PCA plot of assembled mt genomes. ML phylogenetic tree were constructed using SNPs after filtering loci with minor allele frequencies (MAFs) < 0.005 and missing calls > 20%. In PCA plots, samples of different cytoplasmic types were highlighted as dots in different colors. In phylogenetic tree, the cytoplasmic type of each sample was annotated at outer circle as a vetical bar highlighted in different colors. Labels for each sample in phylogenetic tree were also highlighted with four other colors corresponding to groups as follows: black, natural B. napus; red, synthetic B. napus; yellowgreen, B. olracea; cyan, B. rapa