四川山胡椒叶绿体基因组特征及山胡椒属系统发育

Characterization of the Chloroplast Genome of Lindera setchuenensis and Phylogenetics of the Genus Lindera

【目的】四川山胡椒具有重要的药用价值,开展叶绿体基因组研究对山胡椒属物种鉴定、遗传多样性分析和资源保护具有重要的理论和实践意义。【方法】基于Illumina HiSeq 2000高通量测序平台进行测序,从头组装了完整的四川山胡椒叶绿体基因组,并对其基因组结构、基因构成及序列重复和系统发育进行分析。【结果】四川山胡椒叶绿体基因组全长152851 bp,呈典型的四分结构,共编码125个基因,其中蛋白编码基因81个,tRNA基因36个,rRNA基因8个;编码基因的鸟嘌呤和胞嘧啶碱基的出现频率GC3s为27.96%,21个最优密码子中有20个以A/U(T)结尾;27对长序列重复中,正向重复和回文重复分别占比44%和41%,长度为30 bp和33 bp的序列分别占44%和30%;181个SSR位点中,A/T单碱基重复占68%,位于基因间区的占55%;鉴定了6个高变区(petA-psbJ、trnH-psbA、petK-psbI、ccsA-ndhD、rpl32-trnL和ycf1);系统发育分析显示,山胡椒属分为5个聚类组,四川山胡椒与黑壳楠亲缘关系最近。【结论】四川山胡椒叶绿体基因组结构保守,偏好以A或U(T)结尾的密码子;鉴定的高变区和SSR位点可作为山胡椒属物种鉴定的DNA条形码。研究结果可为山胡椒属分子标记开发、系统进化研究及优良品种选育提供参考。

【Objective】Lindera setchuenensis has important medicinal value.Researches of chloroplast genome possess essential theoretical and practical significance for species identification,analysis of genetic diversity and resource protection of the genus Lindera.【Method】The complete chloroplast genome of L.setchuenensis was sequenced based on Illumina HiSeq 2000 platform,and was assembled through de novo.The genome structure,gene composition,repeats and phylogeny were analyzed.【Result】The chloroplast genome of L.setchuenensis exhibited a typical quadripartite structure.A total of 125 functional genes were detected,including 81 protein coding genes,36 tRNA genes,and eight rRNA genes.Frequency of guanine and cytosine bases(GC3s)of the genome encoding genes was 27.96%,20 codons were ended with A/U(T)among 21 optimal codons.Among the 27 pairs of long repeats,forward repeats and palindromic repeats accounted for 44%and 41%respectively,and the length of 30 bp and 33 bp accounted for 44%and 30%respectively.Among the 181 SSRs,68%were A/T repeats and 55%were located in the intergenic regions.Comparing the chloroplast genomes of the genus Lindera,it was indicated that six hyper-variable loci,petA-psbJ,trnH-psbA,petK-psbI,ccsA-ndhD,rpl32-trnL,and ycf1,could potentially be used as DNA barcodes candidates for species identification.Phylogenetic analysis revealed that the genus Lindera was divided into five clades.L.setchuenensis presented the closest relationship with L.megaphylla.【Conclusion】The structure of chloroplast genome of L.setchuenensis is conservative and prefers codons ending with A or U(T).The hyper-variable regions and SSR loci can be used as DNA barcoding for species identification.The results provide a basis for the development of molecular markers,phylogeny and breeding of elite varieties of Lindera plants.