Genomic Studies On Brassica Nigra And Comparative Genomic Analysis On Brassica Species

Including numerous staple crops,such as rapeseed(B.napus,AACC),turnip(B.rapa,AA),cabbage(B.oleracea,CC),and mustards(B.nigra,BB,B.juncea,AABB,B.carinata,BBCC),Brassica species in'U triangle' are both economically and biologically important in the Brassicaceae family.What's more,they are also important in polyploidy study as recurrent polyploidization events occurred during their evolution.Comparative genomic studies on chromosome organization and homeologous genes retention among these species will provide useful genetic information for Brassica breeding and uncover how polyploidy evolve during diploidization.Genome sequences of B.rapa(AA),B.oleracea(CC),B.napus(AACC),B.nigra(BB)and B.juncea(AABB)have been released,which provide very important information of Brassica species and make the genome-wide comparative analysis possible.However,the present B.nigra chromosome sequence was connected with genetic map of B.juncea,hindering the comparative analysis of the B genome.Here we present a new chromosome-level B.nigra assembly constructed with Hi-C connections,and the structure variations compared with other Brassica species.We identified structure variations of B subgenome in B.juncea,and found the chromosome relationships among Brassica A,B and C genomes.To further understand the homeologous genes evolution during diploidization,we also compared the homeologous genes retention in the three basic Brassica diploids and homologous gene evolution in Brassica allotetraploids.We sequenced a natural B.nigra line on Illumina Hiseq platform at an ultra-high depth,and assembled a draft assembly.Then,we further improved this assembly to chromosome-length with Hi-C and finally produced an assembly of 484 Mb,of which 393 Mb were anchored onto 8 chromosomes,taking 81.26%of the assembly.This assembly have high coverage and identitity with B.nigra BAC and EST sequences,as well as more than 80%map rate with RNA-seq data in this study.Compared with the previously published version,our B.nigra assembly has both higher coverage and map rate when aligned with whole genome sequencing reads from a third party.Finally,with this high-quality assembly,we identified 51,829 genes and 47%repeat.We compared the B.nigra genome and B subgenome of B.juncea,revealing comprehensive chromosome variations in the B subgenome,which have lower gene density and higher TE content.We also compared the collinearity between Brassica A,B,and C genomes,and identified their chromosome relationship.Furthermore,we identified the variations in Brassica AJC genomes after their divergence,which showed that A genome remains closer to their common ancestor.We found similar functionally preferential retention of homeologous genes in B.nigra as its sister species and other plant paleopolyploids.Genes with the function of"transcriptional regulation","biosynthetic process"and"transport"were preferentially retained,while"DNA repair"and"response to stimulus"related genes were more likely to remain single-copy.Furthermore,we found that transcriptional regulatory homeologous pairs have higher sequence divergence and more likely to be simutaneously lowly expressed.In Brassica allotetraploids,we found transcriptional regulatory genes is more conserved than other genes,indicating stronger puryfying selection on transcription factors in neopolyploid.By comparing homeologous genes retention in the three basic Brassica diploids,we found prevalent difference.What's more,there seems no functional preference of the differentially retained genes.Homologous genes retained in different copies in three species also didn't show significant difference on expression level.In summary,our work presents a chromosome-level assembly of B.nigra,which provides a useful reference genome for other studies.The comprehensive comparative analysis of the Brassica genomes and homeologous genes also promote our understanding of Brassica and polyploid evolution.