| Sinapis belongs to the tribe Brassiceae in Brassicaceae,with a close evolutionary relationship with Brassica,including two important species S.alba(2n = 24)and S.arvensis(2n = 18).The seeds of S.alba are widely used as condiments and traditional medicine.S.arvensis usually grows in rapeseed and wheat field and is known as a weed in agricultural production.They both have desirable agronomic traits,such as low content of erucic acid and glucosinolate,tolerance or resistance to drought,disease,pests,crack angle,etc.,of which they have become important wild resources for the genetic improvement and breeding of Brassica oil and vegetable crops.Previous studies on cytology,morphology and molecular markers have suggested that S.arvensis is closely related to B.nigra with the same ancestor,while S.arvensis has a relative distant relationship with S.alba.In this study,we performed whole genome sequencing,chromosome-level genome assembly and phylogenomics analysis of B.nigra,S.alba and S.arvensis,revealing the origin and evolutionary relationship of them.At the same time,the release of genomic information will lay the foundation for the effective utilization of excellent genes in the two species genetic improvement of Brassica cultivars.The main findings are as follows:1.Construction of high-quality chromosome-scale genome.PacBio long reads,MGI short reads and Hi-C data were used to assemble three genomes.Finally,we obtain genome reference of B.nigra(519.23Mb),S.abla(439.17Mb)and S.arvensis(452.28Mb)and Contig N50 were 15.67 Mb,7.44 Mb and 7.93 Mb,respectively.In addition,multiple evaluation methods showed high completeness and accuracy of three genome assemblies.2.Repetitive sequences and gene annotation.First,the repetitive sequences of the genome were annotated by a combination of ab initio prediction and homologous sequence alignment.The results showed that the repetitive sequences accounted for 57.53%,58.33% and 55.12% of the total genome in B.nigra,S.alba and S.arvensis respectively.Subsequently,ab initio annotation,homology annotation and RNA-seq data assisted annotation were integrated for gene prediction.A total of 54,855,41,127 and 48,463 protein-coding genes were annotated respectively,and 93.46%,95.05%,and 94.97% of genes were annotated by at least one functional database.3.Comparative genomics analysis.The result of phylogenetic tree shows that Sinapis diverged from the ancestors of Brassica and Raphanus at about 12.54 million years ago(Mya),and S.arvensis and B.nigra were in the same evolutionary branch and the divergence time between them occurred about6.67 Mya.In addition to two WGD events(At-α-WGD and At-β-WGD)shared with A.thaliana,Sinapis also shared a WGT event(Br-WGT)with Brassica and Raphanus about20.28 Mya.4.Genomic structure and collinearity analysis.The result of collinearity analysis based on Brassiceae primordia karyotype(translocation Proto-Calepineae Karyotype: tPCK)shows that S.alba,S.arvensis,B.rapa,B.oleracea,B.nigra and R.sativus have good genome collinearity,especially between B.rapa and B.oleracea,S.arvensis and B.nigra.In addition,two chromosomes of S.alba have completely collinear with two of tPCK,and S.alba shows three colinear chromosomes with R.sativus.5.Subgenome dominance analysis.A total of 26,039 ～ 29,078 subgenomic collinearity genes were detected in six genomes of Brassiceae(B.rapa,B.nigra,B.oleracea,R.sativus,S.alba and S.arvensis),of which44.86% ～ 43.60%,29.83% ～ 30.34% and 25.32% ～ 26.36% were classified as LF,MF1 and MF2 subgenomes,respectively.The average gene density of LF,MF1 and MF2 were 0.459,0.312 and 0.269.In addition,32.9% ～ 36.9%,23.4% ～ 27.5% and 22.7% ～ 27.5% of homologous genes in LF,MF1 and MF2 subgenome show expression domiance.Genes located on the LF subgenome showed stronger selection pressure,and genes retained in all three subgenomes have stronger selection pressure.6.Analysis and traceability of the NLR gene of Brassiceae species.A total of 307,123 and 313 NLR genes were identified in B.nigra,S.abla and S.arvensis,respectively.The number of NLR genes in B.nigra and S.arvensis was more than in the other four diploid species,but less than in allotetraploid species.A NLR enriched region was detected in B.nigra(B04),including 64 NLRs,which was collinear with S.arvensis(Sar08),including 76 NLRs,and traced back to two region in different chromosome of R.sativus,B.rapa and B.oleracea.In summary,we completed the whole genome sequencing of B.nigra,S.alba and S.arvensis and obtained high-quality chromosome-scale genome assemblies;defined the phylogenetic relationship among the Sinapis,Brassica and Raphanus.We further confirmed the dominance relationships among MF1,MF2 and LF subgenome after WGT event,and identified NLR enriched region and its origin. |
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