Dataset Information

Complete plastome sequence of Nepenthes mirabilis (Nepenthaceae): a "vulnerable" herb in China.

ABSTRACT: Nepenthes mirabilis (Nepenthaceae) is an erect or climbing (0.5-2 m tall) herb distributed in Africa (Madagascar), south and southeast Asia, North Australia and Pacific Islands (Caroline Islands). There is only one species in China. It grows in wet and sandy soils places throughout forests, grasslands, swamps, mountains, roadsides, wastelands having altitudes that sea level to 400 m. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of N. mirabilis in an effort to provide genomic resources useful for its conservation. The complete plastome is 155,755?bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,415?bp, a Large Single-Copy (LSC) region of 84,997?bp and a Small Single-Copy (SSC) region of 17,928?bp. The plastome contains 113 genes, consisting of 77 unique protein-coding genes, three pseudogenes, 29 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of N. mirabilis is 62.8%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc., and we determined that N. mirabilis 32 and Dionaea muscipula were closely related. The complete plastome sequence of N. 33 mirabilis will provide a useful resource for the conservation genetics of this species as 34 well as for the phylogenetic studies in Caryophyllales.

SUBMITTER: Zhu ZX

PROVIDER: S-EPMC7800567 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Complete plastome sequence of <i>Nepenthes mirabilis</i> (Nepenthaceae): a "vulnerable" herb in China.

Zhu Zhi-Xin ZX Wang Jian-Hua JH Chen Chao-Rui CR Zhao Kun-Kun KK Wang Hua-Feng HF

Mitochondrial DNA. Part B, Resources 20180703 2

<i>Nepenthes mirabilis</i> (Nepenthaceae) is an erect or climbing (0.5-2 m tall) herb distributed in Africa (Madagascar), south and southeast Asia, North Australia and Pacific Islands (Caroline Islands). There is only one species in China. It grows in wet and sandy soils places throughout forests, grasslands, swamps, mountains, roadsides, wastelands having altitudes that sea level to 400 m. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete pla ...[more]

PMID: 33474302

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Project description:BACKGROUND: Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications. RESULTS: The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR). Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony) or as the sister to Pinus (the only conifer representative) in a monophyletic gymnosperm clade (maximum likelihood, bayesian). Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants. CONCLUSION: Although the basic organization of the Welwitschia plastome is typical, its compactness, gene content and high nucleotide divergence rates are atypical. The current lack of additional conifer plastome sequences precludes any discrimination between the gnetifer and gnepine hypotheses of seed plant relationships. However, both phylogenetic analyses and shared genome features identified here are consistent with either of the hypotheses that link gnetophytes with conifers, but are inconsistent with the anthophyte hypothesis.

Dataset Information

Complete plastome sequence of Nepenthes mirabilis (Nepenthaceae): a "vulnerable" herb in China.

Publications

Complete plastome sequence of <i>Nepenthes mirabilis</i> (Nepenthaceae): a "vulnerable" herb in China.

Similar Datasets

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