华中樱叶绿体基因组特征与分子标记

Chloroplast genomic characteristics and molecular markers of Prunus conradinae

【目的】组装华中樱叶绿体基因组并进行序列特征分析和分子标记初步鉴定。【方法】分别应用SPAdes、prodigal v2.6.3、hmmer v3.1b2及aragorn v1.2.38软件进行华中樱叶绿体基因组组装、基因编码区注释、r RNA和t RNA预测。应用OGDRAW软件进行叶绿体基因组图谱绘制。运用DNAMAN软件对26个樱亚属物种和华中樱的叶绿体基因组序列进行多重比对,人工检索华中樱特有的SNP和InDel位点。应用Codon W1.4.2和EMBOSS的cusp软件分析叶绿体基因组中基因的相对同义密码子使用度。【结果】华中樱叶绿体基因组大小为158 019 bp,其中小单拷贝区(Small single copy,SSC)、大单拷贝区(Large single copy,LSC)和反向重复区(Inverted repeat,IR)大小分别为19 247、85 910和52 862 bp,总GC含量为36.7%。华中樱叶绿体基因组共编码130个基因,包括8个核糖体RNA基因、37个转运RNA基因以及85个蛋白编码基因。序列中有SSR位点240个,其中单核苷酸重复位点153个,二核苷酸重复位点12个,三核苷酸重复位点63个,四核苷酸重复位点11个,六核苷酸重复位点1个。通过与另外26种樱亚属植物叶绿体基因组序列进行多重比对,鉴定了华中樱潜在的种特异性SNP位点29个,InDel标记8个。对密码子进行统计可知,该物种的66种密码子编码了21种氨基酸,其中RSCU> 1的密码子共有32个,有29个以A/U结尾,这些密码子结尾具有A/U偏好性。【结论】华中樱叶绿体基因组是典型的环状四分体结构,其与其他蔷薇科植物叶绿体基因组大小相近。挖掘了一批SSR、SNP和InDel标记,可为华中樱谱系地理学、群体遗传学和种间杂种鉴定等研究提供参考。

【Objective】To assemble the chloroplast genome of Prunus conradinae and carry out sequence analysis and preliminary identification of molecular markers.【Method】SPAdes,prodigal v2.6.3,hmmer v3.1b2 and aragorn v1.2.38 software were used to assemble the chloroplast genome,annotate the gene coding region,and predict rRNA and tRNA.The genome map of chloroplast was drawn by OGDRAW.Multiple alignment of chloroplast genome sequences of P.conradinae and 26 subgenus Cerasus species was carried out using DNAMAN software,and the SNP and InDel sites unique to P.conradinae were manually retrieved.Codon W1.4.2 and EMBOSS cusp software were used to analyze the relative synonymous codon usage of genes in chloroplast genome.【Result】The chloroplast genome size of P.conradinae was 158019 bp,including small single copy(SSC),large single copy(LSC)and inverted repeat(IR),which were 19247 bp,85910 bp and 52862 bp,respectively,and the total GC content was 36.7%.The chloroplast genome of P.conradinae encodes 130 genes,including 8 ribosomal RNA genes,37 transport RNA genes and 85 protein-coding genes.There were 240 SSR sites in the sequence,including 153 single nucleotide repeat sites,12 dinucleotide repeat sites,63 trinucleotide repeat sites,11 tetranucleotide repeat sites,and 1 six-nucleotide repeat site.Through multiple alignment with the chloroplast genome sequences of 26 other subgenus Cerasus species,29 potential species-specific SNP sites and 8 InDel markers were identified.According to the statistics of codons,66 codons of this species encode 21 amino acids,of which 32 codons with RSCU>1,29 codons end with A/U,and these codons end with A/U preference.【Conclusion】The chloroplast genome of P.conradinae is a typical ring tetrad structure,which is similar in size to the chloroplast genome of other Rosaceae plants.A number of SSR,SNP and InDel markers have been excavated to provide references for the study of lineage geography,population genetics and interspecific hybrid identification of P.conradinae.