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The complete chloroplast genome sequences of Trapa acornis Nakano (Lythraceae).

ABSTRACT: Trapa L. (Lythraceae), also called water chestnut, is a genus widely distributed in the Old World. With the high edible and medical values, the water chestnut has been cultivated popularly in China since the Tang and Song Dynasties. Among all cultivars, T. acornis Nakano is one of the most current commercial one, which grown in Jiaxing, Zhejiang province, China. However, due to the limited availability of molecular marker resources of T. acornis, we still have difficulty in its identification and utilization. Here, we reported the complete chloroplast genome sequence of T. acornis. The result demonstrated that the chloroplast genome was 155,538 bp in length, consisting of a small single copy (SSC) region of 18,275 bp, a large single copy (LSC) region of 88,492 bp, and two inverted repeat (IR) regions of 24,386 bp. The chloroplast genome contains a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenomic analysis demonstrated the sister relationship between T. acornis and T. bicornis.

SUBMITTER: Yuan Y

PROVIDER: S-EPMC8667907 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequences of Trapa acornis Nakano (Lythraceae).

Yuan Ye Y Huang Zijian Z Shen Meng M Wang Ruisen R Quan Xinhua X Yao Xiangtan X

Mitochondrial DNA. Part B, Resources 20211209 1

Trapa L. (Lythraceae), also called water chestnut, is a genus widely distributed in the Old World. With the high edible and medical values, the water chestnut has been cultivated popularly in China since the Tang and Song Dynasties. Among all cultivars, T. acornis Nakano is one of the most current commercial one, which grown in Jiaxing, Zhejiang province, China. However, due to the limited availability of molecular marker resources of T. acornis, we still have difficu ...[more]

PMID: 34912954

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Project description:BackgroundTrapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time.ResultsThe Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA-atpF and rps2-rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds.ConclusionIn summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.

Dataset Information

The complete chloroplast genome sequences of Trapa acornis Nakano (Lythraceae).

Publications

The complete chloroplast genome sequences of <i>Trapa acornis</i> Nakano (Lythraceae).

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