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Article

Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity

by
Yue Song
1,†,
Lujia Wang
1,†,
Lipeng Zhang
2,
Junpeng Li
1,
Yuanxu Teng
2,
Zhen Zhang
1,
Yuanyuan Xu
1,
Dongying Fan
1,
Juan He
1 and
Chao Ma
1,*
1
Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
2
Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work and should be considered co-first authors.
Horticulturae 2024, 10(11), 1218; https://doi.org/10.3390/horticulturae10111218
Submission received: 19 October 2024 / Revised: 5 November 2024 / Accepted: 13 November 2024 / Published: 18 November 2024
(This article belongs to the Special Issue Genetics and Molecular Breeding of Fruit Tree Species)
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Abstract

The genus Vitis, known for its economically important fruit—grape—is divided into three geographical groups, American, East Asian, and Eurasian, along with a hybrid group. However, previous studies on grape phylogeny using chloroplast genomes have been hindered by limited sample sizes and inconsistent methodologies, resulting in inaccuracies. In this study, we employed the GetOrganelle software with consistent parameters to assemble the chloroplast genomes of 21 grape cultivars, ensuring comprehensive representation across four distinct groups. A comparative analysis of the 21 grape cultivars revealed structural variation, showing chloroplast genome sizes ranging from 160,813 bp to 161,275 bp. In 21 Vitis cultivars, genome annotation revealed 134 to 136 genes, comprising 89 to 91 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Our observations have pinpointed specific occurrences of contraction and expansion phenomena at the interfaces between inverted repeat (IR) regions and single-copy (SC) regions, particularly in the vicinity of the rpl2, ycf1, ndhF, and trnN genes. Meanwhile, a total of 193 to 198 SSRs were identified in chloroplast genomes. The diversification pattern of chloroplast genomes exhibited strong concordance with the phylogenetic relationships of the Euvitis subgenera. Phylogenetic analysis based on conserved chloroplast genome strongly clustered the grape varieties according to their geographical origins. In conclusion, these findings enhance our understanding of chloroplast genome variation in Vitis populations and have important implications for cultivar selection, breeding, and conservation efforts.
Keywords: chloroplast genome; grape; phylogenetic analysis chloroplast genome; grape; phylogenetic analysis

Share and Cite

MDPI and ACS Style

Song, Y.; Wang, L.; Zhang, L.; Li, J.; Teng, Y.; Zhang, Z.; Xu, Y.; Fan, D.; He, J.; Ma, C. Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity. Horticulturae 2024, 10, 1218. https://doi.org/10.3390/horticulturae10111218

AMA Style

Song Y, Wang L, Zhang L, Li J, Teng Y, Zhang Z, Xu Y, Fan D, He J, Ma C. Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity. Horticulturae. 2024; 10(11):1218. https://doi.org/10.3390/horticulturae10111218

Chicago/Turabian Style

Song, Yue, Lujia Wang, Lipeng Zhang, Junpeng Li, Yuanxu Teng, Zhen Zhang, Yuanyuan Xu, Dongying Fan, Juan He, and Chao Ma. 2024. "Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity" Horticulturae 10, no. 11: 1218. https://doi.org/10.3390/horticulturae10111218

APA Style

Song, Y., Wang, L., Zhang, L., Li, J., Teng, Y., Zhang, Z., Xu, Y., Fan, D., He, J., & Ma, C. (2024). Unified Assembly of Chloroplast Genomes: A Comparative Study of Grapes Representing Global Geographic Diversity. Horticulturae, 10(11), 1218. https://doi.org/10.3390/horticulturae10111218

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