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The complete chloroplast genome of Vicia cracca L.

ABSTRACT: Vicia cracca L. is a widespread perennial herb in the Northern Hemisphere. It has purple flowers and leave tendrils for climbing on neighboring vegetation. For knowing the chloroplast genome, a sample's genomic was extracted, sequenced, assembled and annotated. The chloroplast genome of this plant is a circular form of 126,272bp in length with IR loss. After annotation, a total of 108 genes were predicted, of which, 75 encode proteins, 3 rRNA, 30 tRNA. The evolutionary history, inferred using Maximum Likelihood method, indicates that V. cracca was grouped within Vicia in Fabaceae. The complete cp genome will be helpful for further studies on molecular biology, evolution, population genetics, taxonomy or resources protection.

SUBMITTER: Guo Y

PROVIDER: S-EPMC8205000 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundVicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers.ResultsThe whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200-600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters.ConclusionThe complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.

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The complete chloroplast genome of Vicia cracca L.

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