期刊
GENES
卷 13, 期 2, 页码 -出版社
MDPI
DOI: 10.3390/genes13020369
关键词
Carya cathayensis; chloroplast genome; genome skimming; phylogenetic relationship
资金
- National Natural Science Foundation of China [31971641]
- National Key Research and Development Project [2019YFE0118900]
- Zhejiang Provincial Natural Science Foundation of China [LY16C160011]
- Jiyang College of Zhejiang AF University [RQ1911B07]
Carya cathayensis, an economically important nut tree endemic to eastern China, has a cp genome of 160,825 bp with 129 genes, showing signs of positive selection. Phylogenetic analysis reveals that C. cathayensis is closely related to Carya kweichowensis and Carya illinoinensis.
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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