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The complete chloroplast genome and phylogenetic analysis of Gentiana arethusae Burkill (Gentianaceae) from China

ABSTRACT: Abstract Gentiana arethusae Burkill is a perennial herb classified in the Gentianaceae. In this study, the complete chloroplast genome of G. arethusae was sequenced and analyzed. The chloroplast genome is 137,458 bp in length and encodes a total of 116 genes, including 71 protein-coding, 37 tRNA, and eight rRNA genes. The genome has a low GC content of 38.0%. Phylogenetic analysis of the genome of G. arethusae resolved it in a clade with Gentiana obconica and Gentiana veitchiorum. The complete chloroplast genome of G. arethusae will be helpful to study the genetic diversity and phylogenetics of the Gentianaceae.

SUBMITTER: Li S

PROVIDER: S-EPMC8510589 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP).MethodsUsing high throughput sequencing technology, we got the complete nucleotide sequence of the G. lawrencei var. farreri cp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric species G. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well.ResultsThe cp genome of G. lawrencei var. farreri is a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated that G. lawrencei var. farreri is 10,241 bp shorter than its congeneric species G. straminea. Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes, ndhB, ndhF and clpP, have high nonsynonymous to synonymous values. There are 34 SSRs in the G. lawrencei var. farreri cp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with the G. straminea cp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes clearly identified three clades, which indicated the potential of cp genomes in phylogenetics.DiscussionThe "missing" sequence of G. lawrencei var. farreri mainly consistent of ndh genes which could be dispensable under chilling-stressed conditions in the QTP. The complete cp genome sequence of G. lawrencei var. farreri provides intragenic information that will contribute to genetic and phylogenetic research in the Gentianaceae.

Dataset Information

The complete chloroplast genome and phylogenetic analysis of Gentiana arethusae Burkill (Gentianaceae) from China

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