Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

Xiuming Xu; Hechen Huang; Shaoqing Lin; Linwei Zhou; Yuchong Yi; Enwen Lin; Liqing Feng; Yu Zheng; Aiting Lin; Liying Yu; Yingjia Shen; Robert J Henry; Jingping Fang

doi:10.1186/s12870-024-04995-9

Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

BMC Plant Biol. 2024 Apr 25;24(1):331. doi: 10.1186/s12870-024-04995-9.

Authors

Xiuming Xu^#^{1

2}, Hechen Huang^#², Shaoqing Lin¹, Linwei Zhou¹, Yuchong Yi², Enwen Lin¹, Liqing Feng¹, Yu Zheng², Aiting Lin¹, Liying Yu³, Yingjia Shen², Robert J Henry⁴, Jingping Fang^{5

6}

Affiliations

¹ College of Life Science, Fujian Normal University, Fuzhou, 350117, China.
² Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
³ State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
⁴ Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
⁵ College of Life Science, Fujian Normal University, Fuzhou, 350117, China. jinphia@fjnu.edu.cn.
⁶ Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia. jinphia@fjnu.edu.cn.

^# Contributed equally.

Abstract

Background: Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species.

Results: In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum.

Conclusion: Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.

Keywords: Jasminum; Chloroplast genome; Comparative analysis; Jasmine; Phylogenetic tree.

MeSH terms

Evolution, Molecular*
Genetic Variation*
Genome, Chloroplast*
Jasminum* / genetics
Oleaceae / genetics
Phylogeny*

Grants and funding

2023J01508/Natural Science Foundation of Fujian Province