黄桃叶绿体基因组的组装与序列分析

以‘锦绣'黄桃为试材,利用Illumina NovaSeq 6000测定‘锦绣'黄桃的DNA序列,用SPAdes v3.10.1组装叶绿体基因组,以桃树叶绿体基因组为参考,对其进行叶绿体基因组特征和进化树分析,为进一步开展‘锦绣'黄桃遗传与鉴定学研究奠定良好基础。结果表明：‘锦绣'黄桃叶绿体基因组全长为157 786 bp,具有典型的四分体环状结构,GC含量为36.77%,AT含量为63.23%,包括1个大单拷贝区（LSC）、1对反向重复区（IR）和1个小单拷贝区（SSC）,序列长度分别为85 924、26 381、19 100 bp,LSC、IR和SSC区域中的GC含量分别为34.61%、42.58%、30.41%。‘锦绣'黄桃的叶绿体基因组共注释得到130个基因,包括85个蛋白编码基因、37个tRNA基因和8个rRNA基因;按照功能分类将其分为光合作用相关基因、自我复制相关基因、其他基因和未知功能基因4大类,在这些基因中包括18个双拷贝基因,分别是1个NADH脱氢酶亚基基因（ndhB）、4个自我复制基因（rpl2、rpl23、rps12、rps7）、4个rRNA基因（rrn16、rrn23、rrn4.5、rrn5）、7个tRNA基因（trnA-UGC、trnI-CAU、trnI-GAU、trnL-CAA、trnN-GUU、trnR-ACG、trnV-GAC）、2个未知功能蛋白基因（ycf1、ycf2）。在‘锦绣'黄桃叶绿体基因组中查找248个SSR位点,分布在LSC、SSC、IR区域的SSR数量分别为165、44、39个,占比分别为66.53%、17.74%、15.73%,以单核苷酸重复占绝对优势,主要是A/T,其次是三核苷酸类型,其优势重复单元类型是ATA、TAT和TTA。进化树分析表明,‘锦绣'黄桃与桃树（Prunus persica,MH169125.1）亲缘关系最近。本研究建立了适于‘锦绣'黄桃完整叶绿体基因组组装及其特征分析的方法,为‘锦绣'黄桃的鉴定和系统发育研究奠定基础。

Assembly and Sequence Analysis of Chloroplast Genome of Amygdalus persica

In this study, the complete chloroplast genome of Amygdalus persica L. ‘Jinxiu' was assembled and sequenced. Illumina NovaSeq 6000 platform was used to sequence DNA of A. persica L. ‘Jinxiu', and the chloroplast genome was assembled and annotated by SPAdes v3.10.1. We used the chloroplast genome of Prunus persica as the reference, the feature analysis and phylogenetic analysis study were investigated, laying a foundation for the further development of the genetics and identification of A. persica. The total length of the complete A. persica L. ‘Jinxiu' chloroplast genome was 157 786 bp, including typical quadripartite structure, with a GC content of 36.77% and a AT content of 63.23%. The chloroplast genome had a large single copy region (LSC), a pair of inverted repeats (IR), and a small single copy region (SSC), and the sequence length was 85 924 bp, 26 381 bp, and 19 100 bp, with GC contents of 34.61%, 42.58%, 30.41%, respectively. A total of 130 genes were annotated, consisting of 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. The genes were divided into four categories according to the functions, including photosynthesis, self-replication, other genes and genes of unknown function. The genes included 18 double-copy genes, which were the subunit of NADH dehydrogenase gene (ndhB), four self-replication genes (rpl2, rpl23, rps12 and rps7), four rRNA genes (rrn16, rrn23, rrn4.5 and rrn5), seven tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC), two unknown function protein genes (ycf1and ycf2). A total of 248 microsatellites were founded in the chloroplast genome of A. persica L. ‘Jinxiu'. The simple sequence repeats (SSRs) were spaced disproportionately through the chloroplast genome, with the largest number of SSRs distributed in the LSC region, followed by the SSC and IR regions. LSC, SSC and IR regions had 165, 44 and 39 SSRs, respectively. The number of SSRs in LSC, SSC and IR regions was 66.53%, 17.74%, and 15.73%, respectively. The SSRs were mononucleotides, especially for A/T. The second most abundant motif type was the trinucleotide type, especially ATA, TAT and TTA. Phylogenetic analysis showed that ‘Jinxiu' was closely related to the plant of Prunus persica (MW042696.1) This study would provide a method suitable for the assembly of the complete chloroplast genome and the analysis of feature of the whole chloroplast genome of the ‘Jinxiu', which also could provide evidence for its identification and phylogeny of ‘Jinxiu'.