紫叶风箱果叶绿体基因组特征及绣线菊亚科系统发育分析

Chloroplast genome characteristics of Physocarpus opulifolius‘Diabolo’and phylogenetic analysis of the subfamily Spiraeoideae

紫叶风箱果是我国近年来从北美引入的观赏性花灌木。为了明确紫叶风箱果叶绿体基因组结构特征,阐明紫叶风箱果在绣线菊亚科中的分类地位,使用Illumina NovaSeq 6000测序平台对其叶绿体基因组进行测序,并组装、注释到了其完整叶绿体基因组。结果表明:紫叶风箱果叶绿体基因组呈典型的双链环状四分体结构,全长为159131 bp,大单拷贝区(large single copy,LSC)长87582 bp、小单拷贝区(small single copy,SSC)长18829 bp、反向重复区a(inverted repeats a,IRa)和反向重复区b(inverted repeats b,IRb)长26360 bp;共注释到130个基因,包含83个蛋白编码基因,8个核糖体RNA(ribosomal RNA,rRNA)基因,37个转运RNA(transfer RNA,tRNA)基因和2个假基因。共确定12个最优密码子(UUG、AUU、GUU、GUA、UAA、AAA、UCU、UCC、CCU、ACU、GCU、GGU);密码子使用偏好性主要受自然选择影响,突变等因素对其影响较弱。共有27对长序列重复,87个简单重复序列标记(simple sequence repeat,SSR)位点;psbZ、trnG(UCC)、trnfM(CAU)、trnH(GUG)、psbA、rbcL、rpl20、rps12是紫叶风箱果叶绿体基因组中高核苷酸多态性的基因。系统发育结果表明,风箱果属和绣线梅属的物种亲缘关系较近。

Physocarpus opulifolius‘Diabolo’is an ornamental flowering shrub that has been introduced into China from North America in recent years.The aims of this study were to determine the structural characteristics of the chloroplast genome of P.opulifolius‘Diabolo’and to clarify its taxonomic status within the subfamily Spiraeoideae.The chloroplast genome of P.opulifolius‘Diabolo’was sequenced on the Illumina NovaSeq 6000 sequencing platform,and the complete chloroplast genome was assembled and annotated.The chloroplast genome of P.opulifolius‘Diabolo’had a typical quadripartite structure,with a total length of 159131 bp,large single copy(LSC)length of 87582 bp,small single copy(SSC)length of 18829 bp,and inverted repeats a(IRa)and inverted repeats b(IRb)length of 26360 bp.A total of 130 genes were annotated,including 83 protein-coding genes,8 ribosomal RNA(rRNA)genes,37 transfer RNA(tRNA)genes,and 2 pseudogenes.Twelve codons(UUG,AUU,GUU,GUA,UAA,AAA,UCU,UCC,CCU,ACU,GCU,GGU)were determined.The codon usage bias was mainly affected by natural selection,and mutation was a weak influencing factor.Twenty-seven pairs of long sequence repeats and 87 simple sequence repeat loci were detected.The genes with high nucleotide polymorphism in the chloroplast genome of Physocarpus opulifolius‘Diabolo’were psbZ,trnG(UCC),trnfM(CAU),trnH(GUG),psbA,rbcL,rpl20 and rps12.The results of the phylogenetic analysis showed that Physocarpus is closely related to the genus Neillia.