Dataset Information

Characterization of the complete chloroplast genome sequence of Galinsoga parviflora and its phylogenetic implications.

ABSTRACT: Galinsoga parviflora is an invasive weed in southwest of Chinese agricultural systems and commonly used as medicine and food. In this study, the complete chloroplast genome of the G. parviflora was assembled from the whole genome Illumina sequencing data. The circular genome is 151,811 bp in size, which composed of one large single-copy (LSC) and one small single-copy (SSC) regions of 83,594 bp and 18,141 bp, respectively, and separated by a pair of inverted repeat (IR) regions of 25,038 bp each. It encodes a total of 113 gene species (80 protein-coding, 29 tRNA, and four rRNA species), in which 19 of them with double copies. The overall GC content is 37.7% while the GC content of the LSC, SSC, and IR regions are 35.8%, 31.3%, and 43.1%, separately. Phylogenetic analysis indicated that Galinsoga parviflora was closely related to Galinsoga quadriradiata.

SUBMITTER: Zhang Z

PROVIDER: S-EPMC7687395 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome sequence of Galinsoga parviflora and its phylogenetic implications.

Zhang Zhiyong Z Chen Ying Y Jiang Xuebo X Zhu Piao P Zeng Yanling Y Tang Tianming T Li Ling L

Mitochondrial DNA. Part B, Resources 20190710 2

Galinsoga parviflora is an invasive weed in southwest of Chinese agricultural systems and commonly used as medicine and food. In this study, the complete chloroplast genome of the G. parviflora was assembled from the whole genome Illumina sequencing data. The circular genome is 151,811 bp in size, which composed of one large single-copy (LSC) and one small single-copy (SSC) regions of 83,594 bp and 18,141 bp, respectively, and separated by a pair of inverted repeat (IR) regions of ...[more]

PMID: 33365429

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Project description:Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.

Dataset Information

Characterization of the complete chloroplast genome sequence of Galinsoga parviflora and its phylogenetic implications.

Publications

Characterization of the complete chloroplast genome sequence of <i>Galinsoga parviflora</i> and its phylogenetic implications.

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