The Complete Chloroplast Genome of Baccaurea ramiflora Lour. Cultivar Ha Chau (Phyllanthaceae, Malpighiales)

IF 2.3 2区生物学 Q2 ECOLOGY

Ecology and Evolution Pub Date : 2025-03-18 DOI:10.1002/ece3.71145

Pham Anh Thi Nguyen, Hanh An Nguyen, Hoang Dang Khoa Do, Do Tan Khang

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Abstract

Baccaurea ramiflora cultivar Ha Chau is a specialty fruit in Can Tho City, Viet Nam, and exhibits a potential economic value. However, its genomic data have not been reported. In this study, we sequenced and characterized the complete chloroplast genome of B. ramiflora cultivar Ha Chau using the Illumina sequencing platform, which has a quadripartite structure, including a large single copy (LSC), a small single copy (SSC), and two inverted repeat (IR) regions. The size of the genome was 161,378 bp (made up of 36.7% GC content), which was composed of an 89,801 bp LSC (34.3% GC), an 18,833 bp SSC (30.8% GC), and two 26,372 bp IR (42.7% GC) regions. The newly sequenced chloroplast genome contained 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Notably, the infA gene contained an internal stop codon whereas only rps16 exon2 remained in the complete chloroplast genome of B. ramiflora cultivar Ha Chau. Comparative genomic analyses indicated a high similarity of the chloroplast genome among B. ramiflora individuals regarding genome structure and gene content. However, B. ramiflora cultivar Ha Chau exhibited a lower pairwise identity in comparison with its counterparts. Further phylogenetic analysis also confirmed the sister relationship between B. ramiflora cultivar Ha Chau and other B. ramiflora individuals. This study provides initial genomic data for further studies examining evolutionary history, molecular markers, and genetic populations of B. ramiflora cultivar Ha Chau and its related species in Phyllanthaceae.

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苎麻百合（Baccaurea ramiflora）栽培品种 Ha Chau 是越南芹苴市的特产水果，具有潜在的经济价值。然而，其基因组数据尚未见报道。在本研究中，我们利用 Illumina 测序平台测序并鉴定了苧麻栽培品种 Ha Chau 的完整叶绿体基因组，该基因组具有四方结构，包括一个大单拷贝（LSC）、一个小单拷贝（SSC）和两个反向重复（IR）区。基因组大小为 161,378 bp（GC 含量为 36.7%），由一个 89,801 bp 的 LSC（GC 含量为 34.3%）、一个 18,833 bp 的 SSC（GC 含量为 30.8%）和两个 26,372 bp 的 IR（GC 含量为 42.7%）区域组成。新测序的叶绿体基因组包含 79 个蛋白质编码基因、30 个 tRNA 基因和 4 个 rRNA 基因。值得注意的是，infA 基因含有一个内部终止密码子，而在 B. ramiflora 栽培品种 Ha Chau 的完整叶绿体基因组中只保留了 rps16 外显子 2。基因组比较分析表明，在叶绿体基因组结构和基因含量方面，苎麻叶绿体基因组在苎麻个体间具有很高的相似性。然而，与同类品种相比，B. ramiflora 栽培品种 Ha Chau 的配对一致性较低。进一步的系统发育分析也证实了下洲 B. ramiflora 栽培品种与其他 B. ramiflora 个体之间的姊妹关系。本研究为进一步研究苎麻属植物 Ha Chau 栽培品种及其相关物种的进化历史、分子标记和遗传种群提供了初步的基因组数据。

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来源期刊

Ecology and Evolution ECOLOGY-

CiteScore

4.40

自引率

3.80%

发文量

1027

审稿时长

3-6 weeks

期刊介绍： Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment. Ecology and Evolution gives prompt and equal consideration to papers reporting theoretical, experimental, applied and descriptive work in terrestrial and aquatic environments. The journal will consider submissions across taxa in areas including but not limited to micro and macro ecological and evolutionary processes, characteristics of and interactions between individuals, populations, communities and the environment, physiological responses to environmental change, population genetics and phylogenetics, relatedness and kin selection, life histories, systematics and taxonomy, conservation genetics, extinction, speciation, adaption, behaviour, biodiversity, species abundance, macroecology, population and ecosystem dynamics, and conservation policy.