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. 2024 Nov 11;51(1):1140.
doi: 10.1007/s11033-024-10046-1.

The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae)

JiaZhou Shi  1 , XiaoYing Chen  1 , YiYao Jing  1 , Yonggang Yan  1 , Gang Zhang  1 , BingYue Yang  2 , Liang Peng  3
Affiliations

The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae)

JiaZhou Shi et al. Mol Biol Rep. .

Abstract

Background: Rubia alata Wall (R. alata) and Rubia ovatifolia Z. Ying Zhang (R. ovatifolia) are unique medicinal plants native to China. Sequencing their chloroplast genomes is important for understanding species differentiation and establishing phylogenetic relationships.

Methods and results: The chloroplast genomes of R. alata and R. ovatifolia were sequenced using the Illumina HiSeq platform. The chloroplast genome of R. alata is 154,973 base pairs (bp) in length, containing a large single-copy region (LSC) of 84,801 bp, a small single-copy region (SSC) of 17,138 bp, and a pair of inverted repeats (IRs) of the same length. The length of the chloroplast genome, LSC, SSC, and IR regions of R. ovatifolia is 26,517 bp, 84,716 bp, 17,116 bp and 26,517 bp, respectively. Codon usag e analysis revealed that R. alata had the highest frequency of Aspartic acid (Asp) (1650 occurrences) in protein-coding sequences (CDS), while R. ovatifolia showed the highest frequency of Tyrosine (Try) (1479 occurrences). Comparative analysis of chloroplast genomes across seven species from the genus Rubia identified the most divergent coding regions, including rps16, psbI-trns-CGA, and petN, while plastid rRNAs were the most conserved. Phylogenetic analysis showed R. alata clustering with R. cordifolia (66.3% support), and R. ovatifolia clustering with Rubia podantha (100% support).

Conclusions: These findings enhance our understanding of the chloroplast genome structure in Rubia species and provide molecular information for the future development and utilization of R. alata and R. ovatifolia resources.

Keywords: Rubia alata Wall; Rubia ovatifolia Z. Ying Zhang; Chloroplast genome; Phylogenetic analysis.

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Conflict of interest statement

Declarations Competing interests The authors declare no competing interests. Ethical approval and consent to participate The authors confirm that all methods comply with local and national regulations. Consent for publication This manuscript has been posted as a preprint on Research Square with https://doi.org/10.21203/rs.3.rs-3896731/v1, which is available from: https://www.Researchsquare.com/article/rs-3896731/v1.

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