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The complete chloroplast genome of Melanosciadium pimpinelloideum (Apiaceae), an endemic species of China.

ABSTRACT: Melanosciadium pimpinelloideum de Boiss. is an endemic species of China. Here, the complete chloroplast genome of M. pimpinelloideum is determined. The whole genome size is 164,431 bp in length, composed of a pair of inverted repeats (IRs) of 35,211 bp, a large single-copy region (LSC) of 76,444 bp and a small single-copy region (SSC) of 17,565 bp. The genome contains 136 genes, including 91 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis with the reported chloroplast genomes showed that M. pimpinelloideum and P. rhomboidea var. tenuiloba formed a well-supported clade, which nested in Angelica species. Logically, the result corroborated the previous treatment of P. rhomboidea var. tenuiloba.

SUBMITTER: Tan JB

PROVIDER: S-EPMC7782880 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Melanosciadium pimpinelloideum (Apiaceae), an endemic species of China.

Tan Jin-Bo JB

Mitochondrial DNA. Part B, Resources 20200609 3

Melanosciadium pimpinelloideum de Boiss. is an endemic species of China. Here, the complete chloroplast genome of M. pimpinelloideum is determined. The whole genome size is 164,431 bp in length, composed of a pair of inverted repeats (IRs) of 35,211 bp, a large single-copy region (LSC) of 76,444 bp and a small single-copy region (SSC) of 17,565 bp. The genome contains 136 genes, including 91 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analys ...[more]

PMID: 33457795

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Project description:BackgroundThe genus Sanicula comprises ca. 45 taxa, widely distributed from East Asia to North America, which is a taxonomically difficult genus with high medicinal value in Apiaceae. The systematic classification of the genus has been controversial for a long time due to varied characters in key morphological traits. China is one of the most important distributed centers, with ca. 18 species and two varieties. At present, chloroplast genomes are generally considered to be conservative and play an important role in evolutionary relationship study. To investigate the plastome evolution and phylogenetic relationships of Chinese Sanicula, we comprehensively analyzed the structural characteristics of 13 Chinese Sanicula chloroplasts and reconstructed their phylogenetic relationships.ResultsIn present study, four newly complete chloroplast genome of Sanicula taxa by using Illumina sequencing were reported, with the typical quadripartite structure and 155,396-155,757 bp in size. They encoded 126 genes, including 86 protein-coding genes, 32 tRNA genes and 8 rRNA genes. Genome structure, distributions of SDRs and SSRs, gene content, among Sanicula taxa, were similar. The nineteen intergenic spacers regions, including atpH-atpI, ndhC-trnM, petB-petD, petD-rpoA, petN-psbM, psaJ-rpl33, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-psbD, trnF-ndhJ, trnH-psbA, trnN-ndhF, trnS-psbZ, trnS-trnR, trnT-trnF, trnV-rps12, ycf3-trnS and ycf4-cemA, and one coding region (ycf1 gene) were the most variable. Results of maximum likelihood analysis based on 79 unique coding genes of 13 Chinese Sanicula samples and two Eryngium (Apiaceae-Saniculoideae) species as outgroup taxa revealed that they divided into four subclades belonged to two clades, and one subclade was consistent with previously traditional Sanicula section of its system. The current classification based on morphology at sect. Sanicla and Sect. Tuberculatae in Chinese Sanicula was not supported by analysis of cp genome phylogeny.ConclusionsThe chloroplast genome structure of Sanicula was similar to other angiosperms and possessed the typical quadripartite structure with the conserved genome arrangement and gene features. However, their size varied owing to expansion/contraction of IR/SC boundaries. The variation of non-coding regions was larger than coding regions of the chloroplast genome. Phylogenetic analysis within these Chinese Sanicula were determined using the 79 unique coding genes. These results could provide important data for systematic, phylogenomic and evolutionary research in the genus for the future studies.

Dataset Information

The complete chloroplast genome of Melanosciadium pimpinelloideum (Apiaceae), an endemic species of China.

Publications

The complete chloroplast genome of <i>Melanosciadium pimpinelloideum</i> (Apiaceae), an endemic species of China.

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