Park SeongJun, Park SeonJoo
Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsangbuk-do, Republic of Korea.
Genes (Basel). 2024 Dec 3;15(12):1567. doi: 10.3390/genes15121567.
BACKGROUND/OBJECTIVES: is distributed in Korea, China, and Japan. It was first identified as the genus and then reclassified as by Kitagawa. Some species are used as herbal medicine and are often confused with the similar form . In this study, we analyzed the cp genome of and conducted comparative analyses with the cp genomes of related taxa.
We extracted gDNA from fresh leaves and sequenced it using Illumina HiSeq2500. For the chloroplast genome assembly, de novo assembly was performed using Velvet v1.2.07. For the annotation, GeSeq and NCBI BLASTN were used. Afterwards, related taxa were analyzed using programs such as DnaSP and MISA.
was excluded from the study on the chloroplast (cp) genome in because it was classified as in China. Therefore, this study aimed to analyze the cp genome of for the first time and its location within the genus . The complete cp genome of was 154,755 bp in length, including a pair of inverted repeats, each 26,255 bp, a large single-copy region of 84,581 bp, and a small single-copy region of 17,664 bp. The cp genome comprised 79 protein-coding, 30 tRNA, and 4 rRNA genes. Furthermore, six regions of high nucleotide diversity were identified in the genus . In the genus , 1630 repeats that can serve as markers were also identified. Eight protein-coding genes with high K/K values were under positive selection in the . Our phylogenetic analyses suggest that was positioned with high bootstrap support within the of the tribe , specifically in the southern Palearctic subclade.
In this study, the chloroplast genome was sequenced and assembled. The genus formed a monophyletic group; however, as not all the species were included in this study, further research is necessary. This study can serve as foundational data not only for but also for the tribe Oenantheae.
背景/目的：[该植物名称]分布于韩国、中国和日本。它最初被鉴定为[属名1]属，后被北川重新分类为[属名2]属。一些[该植物名称]物种被用作草药，且常与相似形态的[类似植物名称]混淆。在本研究中，我们分析了[该植物名称]的叶绿体基因组，并与相关类群的叶绿体基因组进行了比较分析。
我们从新鲜叶片中提取基因组DNA（gDNA），并使用Illumina HiSeq2500对其进行测序。对于叶绿体基因组组装，使用Velvet v1.2.07进行从头组装。对于注释，使用GeSeq和NCBI BLASTN。之后，使用DnaSP和MISA等程序对相关类群进行分析。
由于在中国它被分类为[另一植物名称]，所以[该植物名称]被排除在20[年份]关于叶绿体（cp）基因组的研究之外。因此，本研究旨在首次分析[该植物名称]的叶绿体基因组及其在[属名2]属中的位置。[该植物名称]的完整叶绿体基因组长度为154,755 bp，包括一对长度均为26,255 bp的反向重复序列、一个84,581 bp的大单拷贝区域和一个17,664 bp的小单拷贝区域。该叶绿体基因组包含79个蛋白质编码基因、30个tRNA基因和4个rRNA基因。此外，在[属名2]属中鉴定出六个高核苷酸多样性区域。在[属名2]属中，还鉴定出1630个可作为标记的重复序列。在[该植物名称]中有八个具有高K/K值的蛋白质编码基因受到正选择。我们的系统发育分析表明，[该植物名称]在族[族名]的[亚族名]中以高自展支持率定位，具体位于古北界南部亚分支。
在本研究中，对[该植物名称]的叶绿体基因组进行了测序和组装。[属名2]属形成了一个单系类群；然而，由于本研究未涵盖所有[该植物名称]物种，因此有必要进一步研究。本研究不仅可为[该植物名称]，也可为水芹族提供基础数据。
