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Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Riwa Mahai1, Rongpeng Liu1, Xiaolang Du1, Zejing Mu1, Xiaoyun Wang1,*, Jun Yuan2,*

1 Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
2 College of Life Sciences, Jiangxi University of Chinese Medicine, Nanchang, 330004, China

* Corresponding Authors: Xiaoyun Wang. Email: email; Jun Yuan. Email: email

(This article belongs to the Special Issue: Recent Research Trends in Genetics, Genomics, and Physiology of Crop Plants)

Phyton-International Journal of Experimental Botany 2024, 93(6), 1203-1219. https://doi.org/10.32604/phyton.2024.051559

Abstract

Rosaceae represents a vast and complex group of species, with its classification being intricate and contentious. The taxonomic placement of many species within this family has been a subject of ongoing debate. The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae. The cp genomes, varying in size from 153,366 to 159,895 bp, followed the typical quadripartite organization consisting of a large single-copy (LSC) region (84,545 to 87,883 bp), a small single-copy (SSC) region (18,174 to 19,259 bp), and a pair of inverted repeat (IR) regions (25,310 to 26,396 bp). These genomes contained 132–138 annotated genes, including 87 to 93 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes using MISA software, 52 to 121 simple sequence repeat (SSR) loci were identified. D. arbuscular contained the least of SSRs and did not have hexanotides, A. lineata contained the richest SSRs. Long terminal repeats (LTRs) were primarily composed of palindromic and forward repeat sequences, meanwhile, The richest LTRs were found in Argentina lineata. Except for Argentina lineata, Fragariastrum eriocarpum, and Prunus trichostoma, which varied in gene type and position on both sides of the boundary, the remaining species were found to be mostly conserved according to IR boundary analysis. The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1, indicating that this gene was primarily subjected to positive selection during evolution. Additionally, 9 hotspots of variation were identified in the LSC and SSC regions. Phylogenetic analysis confirmed the scientific validity of the genus Prunus L. sensu lato (s.l.) within the Rosaceae family. The separation of the three genera Argentina Hill, Fragariastrum Heist. ex Fabr. and Dasiphora Raf. from Potentilla L. may be a more scientific classification. These results offer fresh perspectives on the taxonomy of the Rosaceae.

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APA Style
Mahai, R., Liu, R., Du, X., Mu, Z., Wang, X. et al. (2024). Comparative and phylogenetic analysis of the complete chloroplast genomes of 19 species in rosaceae family. Phyton-International Journal of Experimental Botany, 93(6), 1203-1219. https://doi.org/10.32604/phyton.2024.051559
Vancouver Style
Mahai R, Liu R, Du X, Mu Z, Wang X, Yuan J. Comparative and phylogenetic analysis of the complete chloroplast genomes of 19 species in rosaceae family. Phyton-Int J Exp Bot. 2024;93(6):1203-1219 https://doi.org/10.32604/phyton.2024.051559
IEEE Style
R. Mahai, R. Liu, X. Du, Z. Mu, X. Wang, and J. Yuan "Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family," Phyton-Int. J. Exp. Bot., vol. 93, no. 6, pp. 1203-1219. 2024. https://doi.org/10.32604/phyton.2024.051559



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