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. 2024 Jun 10;15(6):761.
doi: 10.3390/genes15060761.

Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation

Ji Eun Kim  1 , Keyong Min Kim  2 , Yang Su Kim  3 , Gyu Young Chung  4 , Sang Hoon Che  5 , Chae Sun Na  1
Affiliations

Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation

Ji Eun Kim et al. Genes (Basel). .

Abstract

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.

Keywords: Vitis; chloroplast; conservation; genetic diversity; genome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Seed sampling sites for Vitis flexuosa and V. amurensis in South Korea. The indicated colors and shapes identify seeds of each species that were used or unused.
Figure 2
Figure 2
Circular maps representing the complete chloroplast genomes of (A) V. flexuosa and (B) V. amurensis. The center boundary shows the length of each region. Each gene has been color-coded to distinguish its functionality. Genes inside and outside the circle are transcribed in clockwise and counterclockwise directions, respectively, as indicated by the arrows.
Figure 3
Figure 3
Relative synonymous codon usage for amino acids in the protein-coding regions of the chloroplast genomes of the two Vitis species. For each amino acid, the left bar represents V. amurensis and the right one represents V. flexuosa,.
Figure 4
Figure 4
Simple sequence repeats (SSRs) in the chloroplast genomes. X-axes: species and types of SSRs. Y-axes: number of SSRs. (a) Number and types of SSRs. (b) Identification of SSRs in each region. (c) Frequency of SSRs in different repeat class types.
Figure 5
Figure 5
Number of long-repeat sequences in the Vitis chloroplast genomes (F: forward repeats; R: reverse repeats; P: palindromic repeats; C: complementary repeats).
Figure 6
Figure 6
Comparison of boundary positions in LSC, SSC, and IR regions of Vitis. Genes are represented with boxes, and gaps between the genes and boundaries are indicated with the number of bases.
Figure 7
Figure 7
Comparison of three Vitis chloroplast genomes using the mVISTA program. Gray arrows indicate the direction and location of genes. Genomic regions, including non-coding (CNS) and coding regions, are depicted with red, light blue, and blue blocks.
Figure 8
Figure 8
Sliding window analysis of chloroplast genomes of Vitis.
Figure 9
Figure 9
Phylogenetic tree constructed from Vitis chloroplast sequences, and bootstrap values based on 1000 replicates are displayed on each node. The tip label colors represent different categories: black for crop wild relatives (CWRs), green for landraces (native and also-cultivated), pink for subjects in this study, and blue for modern cultivars (criteria by GRIN-Global).
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