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Characterization of the complete chloroplast genome of Gentiana rhodantha (Gentianaceae).

ABSTRACT: The first complete chloroplast genome (cp) sequences of Gentiana rhodantha were reported in this study. The cp genome of G. rhodantha was 148,967 bp in size, with two inverted repeat (IR) regions of 25,760 bp, the large single copy (LSC) region of 79,831 bp, and the small single copy (SSC) region of 17,616 bp. The cp genome contained 112 genes, including 78 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the tribe Gentianeae suggests that G. rhodantha is in a sister clade of other subtribe Gentianinae.

SUBMITTER: Ling LZ

PROVIDER: S-EPMC7748746 | 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.

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Characterization of the complete chloroplast genome of Gentiana rhodantha (Gentianaceae).

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