College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
Aesthetic Education Center, Qingdao University of Science and Technology, Qingdao 266042, China.
Genes (Basel). 2022 Mar 4;13(3):461. doi: 10.3390/genes13030461.
(wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as and , were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between with the , , and . Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
（冬瓜）是葫芦科的重要作物，具有巨大的经济和药用价值。在这里，我们报道了冬瓜完整叶绿体基因组的从头组装和注释，总长度为 156758bp。叶绿体基因组的四分体结构由一个大的单拷贝（LSC）区域组成，长度为 86538bp，一个小的单拷贝（SSC）区域长度为 18060bp，由一对 26080bp 的反向重复（IRa 和 IRb）隔开。与三本科皮葫芦科的其他物种进行比较分析，在核苷酸含量、基因组结构、密码子使用、同义和非同义替换、假定的 RNA 编辑位点、微卫星和寡核苷酸重复方面表现出显著的转换。通过对科内物种的分歧分析发现，LSC 和 SSC 区域比 IR 区域变化更大。观察到明显的 IR 收缩和扩张，表明基因组大小、基因复制和缺失以及假基因的存在存在差异。内含子基因序列，如 和 ，被观察为高度变异区域。基于完整 cp 基因组和 72 个基因的两种系统发育分析表明，与 、 、 之间存在姐妹关系。关于系统发育关系的变异和一致性与以前的研究进行了讨论。冬瓜的 cp 基因组为分子标记的检测、分类学差异的研究以及葫芦科的系统发育推断提供了有价值的遗传信息。
