Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.

IF 1.6 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemical Genetics Pub Date : 2025-08-19 DOI:10.1007/s10528-025-11229-6

Suhas K Kadam, Asif S Tamboli, Jin-Suk Youn, Jae Hong Pak, Yeon-Sik Choo

{"title":"Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.","authors":"Suhas K Kadam, Asif S Tamboli, Jin-Suk Youn, Jae Hong Pak, Yeon-Sik Choo","doi":"10.1007/s10528-025-11229-6","DOIUrl":null,"url":null,"abstract":"<p><p>The chloroplast (Cp) genome offers valuable perceptions into plant evolution, systematics, and phylogenetics. Here we are reporting complete chloroplast genome of Stellaria media (L.) Vill. collected from Dokdo Island, South Korea. The genome, assembled at 6340 × coverage, is 147,329 bp with a typical quadripartite structure, covering two inverted repeat (IR) regions of 25,600 bp and one single copy of large (79,366 bp) and small region (16,763 bp) each. Genome annotation identified 129 genes, including 84 protein-coding genes, 8 rRNA and 37 tRNA genes. In the IR region, ycf3 and clpP1 each contain two introns, while 17 genes, including rpl2, trnL-CAA, ycf2, and ndhB are present in duplicate, whereas rps19 is present as a single copy, reflecting structural conservation and evolutionary mechanisms such as intron retention and gene duplication. Comparative genomic analysis revealed substantial variations both among Stellaria species and in the formerly classified Stellaria dichotoma var. lanceolata. Codon usage showed a biasness toward codons ending with A/U, with leucine being most frequently encoded amino acid. Phylogenetic reconstruction based on complete chloroplast genomes positioned S. media within the Alsineae tribe and highlighted monophyletic relationships in the genus. Sliding window analysis identified hypervariable regions, including ycf1, ndhF-rpl32, and trnK-rps16 as potential molecular markers. This study provides crucial perceptions into chloroplast genome evolution, comparative genomics, and phylogeny within Caryophyllaceae, contributing essential data for taxonomic and conservation research. Additionally, multiple lines of evidence, including comparative chloroplast genomics, analyses of long and short repeat sequences, codon usage patterns, and phylogenetic relationships, support the taxonomic revision of inclusion of the genus Myosoton within Stellaria, and the exclusion of Stellaria dichotoma var. lanceolata from the genus Stellaria.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.6000,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemical Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s10528-025-11229-6","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

The chloroplast (Cp) genome offers valuable perceptions into plant evolution, systematics, and phylogenetics. Here we are reporting complete chloroplast genome of Stellaria media (L.) Vill. collected from Dokdo Island, South Korea. The genome, assembled at 6340 × coverage, is 147,329 bp with a typical quadripartite structure, covering two inverted repeat (IR) regions of 25,600 bp and one single copy of large (79,366 bp) and small region (16,763 bp) each. Genome annotation identified 129 genes, including 84 protein-coding genes, 8 rRNA and 37 tRNA genes. In the IR region, ycf3 and clpP1 each contain two introns, while 17 genes, including rpl2, trnL-CAA, ycf2, and ndhB are present in duplicate, whereas rps19 is present as a single copy, reflecting structural conservation and evolutionary mechanisms such as intron retention and gene duplication. Comparative genomic analysis revealed substantial variations both among Stellaria species and in the formerly classified Stellaria dichotoma var. lanceolata. Codon usage showed a biasness toward codons ending with A/U, with leucine being most frequently encoded amino acid. Phylogenetic reconstruction based on complete chloroplast genomes positioned S. media within the Alsineae tribe and highlighted monophyletic relationships in the genus. Sliding window analysis identified hypervariable regions, including ycf1, ndhF-rpl32, and trnK-rps16 as potential molecular markers. This study provides crucial perceptions into chloroplast genome evolution, comparative genomics, and phylogeny within Caryophyllaceae, contributing essential data for taxonomic and conservation research. Additionally, multiple lines of evidence, including comparative chloroplast genomics, analyses of long and short repeat sequences, codon usage patterns, and phylogenetic relationships, support the taxonomic revision of inclusion of the genus Myosoton within Stellaria, and the exclusion of Stellaria dichotoma var. lanceolata from the genus Stellaria.

查看原文本刊更多论文

星属培养基叶绿体基因组的揭示：综合分析、分类意义和进化观点。

叶绿体基因组为植物进化、系统学和系统发育提供了有价值的认识。在这里，我们报道了Stellaria media （L.）的完整叶绿体基因组。斯德。收集自韩国独岛。基因组全长147,329 bp，覆盖面积为6340 ×，具有典型的四分体结构，覆盖两个25,600 bp的反向重复（IR）区域和一个大（79,366 bp）和一个小（16,763 bp）区域。基因组注释鉴定出129个基因，包括84个蛋白质编码基因、8个rRNA和37个tRNA基因。在IR区，ycf3和clpP1各含有2个内含子，rpl2、trnL-CAA、ycf2和ndhB等17个基因以双拷贝形式存在，而rps19以单拷贝形式存在，反映了内含子保留和基因复制等结构守恒和进化机制。比较基因组分析揭示了星属物种之间和以前分类的星属（Stellaria dichotoma var. lanceolata）之间的实质性差异。密码子的使用倾向于以a /U结尾的密码子，其中亮氨酸是编码频率最高的氨基酸。基于完整叶绿体基因组的系统发育重建将S. media定位在alsinineae部落中，并强调了该属的单系关系。滑动窗口分析确定了高变区，包括ycf1、ndhF-rpl32和trnK-rps16作为潜在的分子标记。该研究为石竹科植物叶绿体基因组进化、比较基因组学和系统发育提供了重要的认识，为分类和保护研究提供了重要的数据。此外，多种证据，包括比较叶绿体基因组学、长重复序列和短重复序列分析、密码子使用模式和系统发育关系，支持将Myosoton属包含在Stellaria中，并将Stellaria dichotoma var. lanceolata从Stellaria属中排除的分类修正。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Biochemical Genetics 生物-生化与分子生物学

CiteScore

3.90

自引率

0.00%

发文量

133

审稿时长

4.8 months

期刊介绍： Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses. Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication. Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses. Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods. Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.