Diversified Genomic Organizations In Taxaceae Chloroplast Genomes

Most chloroplast(cp)genomes of land plant contain two copies of large inverted repeat(IR),which might promote homologous recombination to generate isomeric genomic forms.However,IR is highly reduced in conifer cp genomes,the isomeric cp genomes could be generated by their specific inversions mediated by short inverted repeats.Taxaceae,belongs to conifer and loses an IR region thus reduced the cp genome diversity.To unravel the mechanism of IR reduction,we examined the cp genomes organizations of 15 species from four Taxaceae genera,with the cp genome of Taxus cuspidate Siebold&Zuccarini,Taxus fuana Nan Li&R.R.Mill,Taxus wallichiana Zuccarini and Taxus wallichiana var.wallichiana's were firstly sequenced,assembled.Our results illustrated four distinctly isomeric cp genome forms(A,B,C and D)in Taxaceae which were induced by the relative locations and orientations rearrangements of two specific fragments(infA-rps12,?18 kb and trnQ-IR,?34 kb)."trnQ-IR"inversion fragment is flanked by the trnQ-UUG gene,which range from 114 to 560 bp of the 15 Taxaceae species and several pairs of 9-12 bp inverted short repeats specifically residing at the boundaries of the "infA-rps12" fragment.In addition,two isomeric cp genome forms A and B were verified co-existed in 20 individuals of T.cuspidata.We derived a most parsimonious rearrangement scenario of diversified genomic organizations in Taxaceae.The minimum number of inversions from the reference cp genome Cephalotoxus oliveri Masters to the four distinct forms of Taxaceae ranges from three to six.The phylogenetic analysis results showed that Taxaceae were separated into two lineages.One including Taxus,Pseudotaxus and another formed by Amentotaxus and Torreya at the basal position.In this study,we sequenced,assembled and characterized four Taxus species cp genomes.Our study revealed novel insights into the structural diversification and phylogenetic relationships of Taxaceae cp genomes.These results will advance understanding of how the conifer cp genomes diversitied.