Evolution Of Chloroplast Genome And Re-construction Of Phylogenetic Relationships Among The Actinidia

The interspecies relationships within the genus Actinidia remain largely contro-versial as frequent interspecific introgression occurred among the species.Thus,the phylogenetic relationship of this genus needs to be further investigated.With the rapid development of sequencing technology,the chloroplast genome has been widely used for phylogenetic analysis.Noncoding sequences are more suitable than coding se-quences for phylogenetic relationships analysis at species level.In order to acquire more chloroplast genome data,we sequenced and annotated plastid genomes of Actinidia eriantha,A,arguta and A.kolomikta.Nine plastomes of Actinidia were aligned to compare its structure,and molecular markers were developed based on chloroplast intergenic variation sites to reconstruct the phylogenetic relationships among the Actinidia.Main results are as follows:(1)The complete plastome of A.eriantha,A.kolomikta and A.arguta ranging from 156,484 bp to 157,425 bp in length exhibited a typical quadripartite structure,including a pair of IRs(23,829-24,226bp)separated by the LSC(88,093-88,639 bp)and SSC(20,475-20,579 bp)regions.These three cp genomes encoded an identical set of 113 predicted functional genes when duplicated genes were calculated only once,including 79 protein-coding genes,30 transfer RNA(tRNA)genes and four rRNA genes,of which 16 genes were duplicated in IRs and one(trnfM-CAU)was duplicated in LSC.In our analyses,the total number of repeat sequences in the chloroplast ge-nome of A.eriantha,A.arguta and A.kolomikta was 39,25,33 respectively,and the shortest repeat sequences in A.arguta was 60 bp.Additionally,the ycf2,rpl20 and genetic system gene accD were detected under positive selection during its evolution in Actindia by using branch model.(2)The overall sequence identity of nine cp genomes was plotted with mVISTA,twenty-four intergenic spacers were determined with high degrees of divergence and four of them,i.e.ndhF-rps32,ndhC-trn V(UAC),rps16-trnQ(UUG)and trnE(UUC)-trnT(GGU)were used to develop primers to reconstruct phylogenetic re-lationship of Actinidia species.The results indicated that these four cpDNA intergenic spacers could be used to reconstruct the intraspecific relationship with higher resolu-tion compared to previous studies.The phylogenetic trees showed that only the Leiocarpae formed a clade while species from other three sections(Stellatae,Strigosae,Maculatae)formed a monophyletic group.The current infrageneric tax-onomy of Actinidia needs to be revised with much more morphological and molecular data.