Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers

Abstract

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.

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

“…For instance, nine genes were transferred from the SSC to the IR region in Plantago ovata , resulting in an extremely long IR (37.4 kb) [ 26 ] as compared to IR found in the other plastomes, which normally range between 25 and 30 kb [ 42 ]. In contrast, the loss of IR had been reported in the plastomes of Vicia bungei [ 72 ] and 25 durian varieties recently [ 38 ]. Besides long inversion, small-to-medium-sized (<few hundred base pairs) inversion in the plastome was also commonly found in angiosperm.…”

Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species

“…The loss of IR regions likely leads to mechanisms such as increased mutation rates, facilitated genome rearrangements, and altered selection pressures and intron structure, significantly accelerating the rate of evolution of the chloroplast genome [ 23 ]. Numerous studies have shown gene and intron loss, such as the loss of introns from the rps12 and clpP genes in chickpea ( Cicer arietinum ) [ 24 ], loss of the accD gene in Trifolium [ 25 , 26 ], and loss of rpl22 , rps16 , and one intron of clpP in Vicia [ 27 ]. In this study, the rpl22 and infA genes in the Caragana chloroplast genomes were lost ( Figure 2 ).…”

The complete chloroplast genome sequence of Melochia corchorifolia Linnaeus, 1753 (Sterculiaceae)

“… 1994 ; Jo et al. 2022 ). It is important to resolve the phylogenetic relationships of species and their evolution; however, only a few complete chloroplast genome sequences of species in the genus Melochia have been reported.…”