State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
Molecules. 2018 Jun 5;23(6):1358. doi: 10.3390/molecules23061358.
Schousb and are widely distributed edible vegetables and the sources of the Chinese medicine . The complete chloroplast (cp) genome of usually occurs in the inversions of two regions. Hence, the cp genome sequences and structures of species are crucial for the cp genome genetic diversity and evolutionary studies. Hence, in this paper, we have sequenced and analyzed for the first time the cp genome size of Schousb and , which are 149,752 bp and 152,885 bp, with a pair of inverted repeats (IRs) (24,523 bp and 25,003) separated by a large single copy (LSC) region (82,290 bp and 84,610) and a small single copy (SSC) region (18,416 bp and 18,269), respectively. In total, 79 protein-coding genes, 30 distinct transfer RNA (tRNA) genes, four distinct rRNA genes and two pseudogenes were found not only in Schousb but also in the cp genome. Fifty-two (52) and fifty-nine (59) repeats, and seventy (70) and ninety (90) simple sequence repeats (SSRs) were found in the Schousb and cp genomes, respectively. Codon usage analysis showed that leucine, isoleucine, and serine are the most frequent amino acids and that the UAA stop codon was the significantly favorite stop codon in both cp genomes. The two inversions, the LSC region ranging from to and the whole SSC region were found in both of them. The complete cp genome comparison with other species showed that the coding area is more conservative than the non-coding area. The phylogenetic analysis revealed that the gene is a good barcoding marker for identifying different vegetables. These results give an insight into the identification, the barcoding, and the understanding of the evolutionary model of the cp genome.
薤白和小根蒜是广泛分布的食用蔬菜，也是中药的来源。通常， 的完整叶绿体 (cp) 基因组在两个区域的倒位中发生。因此， 种的 cp 基因组序列和结构对于 cp 基因组遗传多样性和进化研究至关重要。因此，在本文中，我们首次对 薤白和小根蒜的 cp 基因组大小进行了测序和分析，它们的大小分别为 149752bp 和 152885bp，具有一对倒置重复 (IR) (24523bp 和 25003)，由一个大的单拷贝 (LSC) 区域 (82290bp 和 84610) 和一个小的单拷贝 (SSC) 区域 (18416bp 和 18269) 隔开。总共发现了 79 个蛋白质编码基因、30 个独特的转移 RNA (tRNA) 基因、4 个独特的 rRNA 基因和 2 个假基因，不仅在 薤白中，而且在 cp 基因组中都有发现。在 薤白和 cp 基因组中分别发现了 52 个和 59 个重复序列、70 个和 90 个简单序列重复 (SSR)。密码子使用分析表明，亮氨酸、异亮氨酸和丝氨酸是最常见的氨基酸，而 UAA 终止密码子是两个 cp 基因组中最受欢迎的终止密码子。两个倒位，即从 到 的 LSC 区域和整个 SSC 区域，在它们两个中都有发现。与其他 种的完整 cp 基因组比较表明，编码区比非编码区更保守。系统发育分析表明， 基因是识别不同蔬菜的良好条形码标记。这些结果为 cp 基因组的鉴定、条形码和进化模型的理解提供了深入的了解。
