College of Environmental and Biological Engineering, Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control for Emerging Contaminants, Key Laboratory of Ecological Environment and Information Atlas (Putian University) Fujian Provincial University, Putian University, Putian, 351100, China.
College of Environmental and Biological Engineering, Putian University, Putian, 351100, China.
Sci Rep. 2024 Aug 13;14(1):18816. doi: 10.1038/s41598-024-69882-7.
The chloroplast genomes of wild loquat can help to determine their place in the history of evolution. Here, we sequenced and assembled two novel wild loquat's chloroplast genomes, one is Eriobotrya elliptica, and the other is an unidentified wild loquat, which we named "YN-1". Their sizes are 159,471 bp and 159,399 bp, respectively. We also assembled a cultivated loquat named 'JFZ', its chloroplast genome size is 159,156 bp. A comparative study was conducted with six distinct species of loquats, including five wild loquats and one cultivated loquat. The results showed that both E. elliptica and "YN-1" have 127 genes, one gene more than E. fragrans, which is psbK. Regions trnF-GAA-ndhJ, petG-trnP-UGG, and rpl32-trnL-UAG were found to exhibit high variability. It was discovered that there was a positive selection on rpl22 and rps12. RNA editing analysis found several chilling stress-specific RNA editing sites, especially in rpl2 gene. Phylogenetic analysis results showed that "YN-1" is closely related to E. elliptica, E. obovata and E. henryi.
野生枇杷的叶绿体基因组有助于确定它们在进化史上的位置。在这里，我们测序并组装了两个新的野生枇杷的叶绿体基因组，一个是椭圆枇杷，另一个是未鉴定的野生枇杷，我们将其命名为“YN-1”。它们的大小分别为 159471bp 和 159399bp。我们还组装了一个名为“JFZ”的栽培枇杷的叶绿体基因组，其大小为 159156bp。我们对六个不同种的枇杷，包括五个野生枇杷和一个栽培枇杷进行了比较研究。结果表明，椭圆枇杷和“YN-1”都有 127 个基因，比枇杷属的 psbK 基因多一个。trnF-GAA-ndhJ、petG-trnP-UGG 和 rpl32-trnL-UAG 区域表现出高度变异性。发现 rpl22 和 rps12 上存在正选择。RNA 编辑分析发现了几个冷胁迫特异性的 RNA 编辑位点，特别是在 rpl2 基因中。系统发育分析结果表明，“YN-1”与椭圆枇杷、宽叶枇杷和石斑枇杷密切相关。
