Dataset Information

The complete chloroplast genome sequence of Metabriggsia ovalifolia W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China.

ABSTRACT: Metabriggsia ovalifolia W. T. Wang is one of the first-class national protected plants endemic to Karst areas in China. In this study, the complete chloroplast genome was sequenced using Illumina pair-end sequencing data. The chloroplast genome was 153,333 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 25,448 bp), separated by a large single copy region (LSC: 84,381 bp) and a small single copy region (SSC: 18,056 bp). The chloroplast genome encodes 131 genes, including 87 protein-coding genes, 36 transfer RNA, and eight ribosomal RNA genes. The overall GC content of the chloroplast genome was 37.55%. M. ovalifolia phylogenetic analysis indicated close relationship with Oreocharis mileensis of Gesneriaceae family. These genomic resources will be helpful for conservation of this endemic plant species.

SUBMITTER: Tian X

PROVIDER: S-EPMC7954431 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of <i>Metabriggsia ovalifolia</i> W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China.

Tian Xiaoling X Wariss Hafiz Muhammad HM

Mitochondrial DNA. Part B, Resources 20210311 3

<i>Metabriggsia ovalifolia</i> W. T. Wang is one of the first-class national protected plants endemic to Karst areas in China. In this study, the complete chloroplast genome was sequenced using Illumina pair-end sequencing data. The chloroplast genome was 153,333 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 25,448 bp), separated by a large single copy region (LSC: 84,381 bp) and a small single copy region (SSC: 18,056 bp). The chloroplast genome encodes 131 genes, includi ...[more]

PMID: 33763595

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Project description:Guizhou Province is one of the most important karst regions of southwest China, with 22 Primulina species. These species are highly habitat-specialized and dependent on the soils of the karst region, and many inter-species classifications are unclear. Therefore, studying the chloroplast genomes and estimating the divergence times of there species can not only provide a better understanding of interspecific relationships but also help to know the species speciation and divergence in the karst environment. So, we sequenced and assembled the chloroplast genomes of nine Primulina species (including six endemic species of Guizhou) and conducted chloroplast genome comparison analysis and phylogenetic study. The chloroplast genome structures of the nine Primulina species were quadripartite with total lengths of 152,869-153,364 base pairs (bp) and GC content of 37.55-37.64%. There are 132 functional genes annotated, respectively. A total of 375 simple sequence repeats and 375 interspersed nuclear elements were identified. The 30 highly preferred codons identified were used at similar frequencies in different species, respectively. A phylogenetic tree constructed on the basis of the 38 chloroplast genomes showed that Primulina species form a monophyletic group. Eleven mutational hotspot regions that could serve as potential molecular markers were identified, of which two regions near the 3' and 5' ends of the ycf1 gene were of appropriate size and can serve as molecular markers for phylogenetic studies of Primulina. The results of molecular clock analyses indicate that the three major branches of Primulina begin to diverge in the Miocene, and the number of species proliferated in the Pliocene and Pleistocene. Most of the species of Primulina in Guizhou Province were formed in the Pleistocene and rapidly diverged within a short period of time. This research study enriches the genetic resource information of Primulina and deepens the understanding of the phylogenetic relationships of the genus.

Project description:BackgroundThe karst regions in South China have an abundance of endemic plants that face high extinction risks. The Chinese Gesneriaceae endemic Paraisometrum mileense ( = Oreocharis mileensis), was presumed extinct for 100 years. After its re-discovery, the species has become one of five key plants selected by the Chinese forestry government to establish a new conservation category for plants with extremely small populations. For conservation purposes, we studied the phylogenetic and population genetic status of P. mileense at the three only known localities in Guangxi, Guizhou and Yunnan.Methodology/principal findingsWe collected 64 samples (52 species) of Oreocharis and 8 samples from three provinces of P. mileense and generated molecular phylogenies, and inferred that P. mileense represents a relatively isolated and derived taxonomic unit within Oreocharis. Phylogeographic results of 104 samples of 12 populations of P. mileense indicated that the populations in Yunnan have derived from those in Guangxi and Guizhou. Based on AFLP data, the populations were found to harbor low levels of genetic diversity (He = 0.118), with no apparent gradient across the species' range, a restricted gene flow and significant isolation-by-distance with limited genetic differentiation among the populations across the three provinces (FST = 0.207, P<0.001). The 10 populations in Yunnan were found to represent two distinct lineages residing at different altitudes and distances from villages.Conclusion/significanceThe low levels of genetic diversity found in P. mileense are perhaps a consequence of severe bottlenecks in the recent past. The distribution of the genetic diversity suggests that all populations are significant for conservation. Current in situ and ex situ measures are discussed. Further conservation actions are apparently needed to fully safeguard this conservation flagship species. Our work provides a model of an integrated study for the numerous endemic species in the karst regions with extremely small populations.

Dataset Information

The complete chloroplast genome sequence of Metabriggsia ovalifolia W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China.

Publications

The complete chloroplast genome sequence of <i>Metabriggsia ovalifolia</i> W. T. Wang (Gesneriaceae), a national key protected plant endemic to Karst areas in China.

Similar Datasets

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