The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis.
The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis.
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DOI：
10.3390/genes13020369
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发表时间：
2022-02-18
期刊：
影响因子：
3.5
通讯作者：
Jin S
中科院分区：
文献类型：
--
作者：
Shen J;Li X;Chen X;Huang X;Jin S
山核桃（Caryacathayensis）是我国东部地区特有的野生坚果树种，是一种重要的经济树种。对C.使用Illumina HiSeq 2500用NGS对cathayensis进行测序，分析，并与其密切相关的物种进行比较。cp基因组长度为160，825 bp，总GC含量为36.13%，呈现由大单拷贝（LSC; 90，115 bp）、小单拷贝（SSC; 18，760 bp）和一对反向重复序列（IR; 25，975 bp）组成的四方结构。基因组包含129个基因，其中蛋白质编码基因84个，tRNA基因37个，rRNA基因8个。共鉴定出252个简单重复序列（SSR）和55个长重复序列。基因选择压力分析表明，rps 15、rpoA、rpoB、petD、ccsA、atpI和ycf 1 -2等7个基因与核桃科其他物种相比可能处于正选择状态。通过对46种植物的系统发育关系分析，推测核桃科植物为单系，C. cathayensis是贵州山核桃（Carya kweichowensis）和美国山核桃（Carya illinoinensis）的姐妹。基因组比较显示，有一个广泛的变异的连接位点，有较高的分歧，在非编码区比编码区。这些结果表明，在系统发育研究的巨大潜力。新鉴定的C. cathayensis为进一步研究这一重要经济种提供了有价值的信息。
Carya cathayensis, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of C. cathayensis was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (rps15, rpoA, rpoB, petD, ccsA, atpI, and ycf1-2) were possibly under positive selection compared with the other Juglandaceae species. Phylogenetic relationships of 46 species inferred that Juglandaceae is monophyletic, and that C. cathayensis is sister to Carya kweichowensis and Carya illinoinensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.
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