A comparative study of the chloroplast genomes of five Lepidium species with high medicinal value
Qian Zhou
A , Yun Chen A , Jilian Wang A , Mingyuan Li A , Weijun Zeng B , Yuzhou Wang A , Yanhong Li B * and Huixin Zhao B *
+ Author Affiliations
- Author Affiliations
A Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, College of Life and Geography Sciences, Kashi University, Kashi, China.
B Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China.
Functional Plant Biology 50(1) 29-45 https://doi.org/10.1071/FP22052
Submitted: 29 March 2022 Accepted: 28 July 2022 Published: 31 August 2022
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Plantgenomics is a rapidly developing field in medicinal plant research. This study analysed the relevant information of chloroplasts genome sequences of five medicinal plants from the genus Lepidium. We sequenced the complete chloroplast (cp) genomes of Lepidium apetalum Willd. and Lepidium perfoliatum Linnaeus., and assessed their genetic profiles against the reported profiles of Lepidium sativum Linnaeus., Lepidium meyenii Walp., and Lepidium virginicum Linn. We found that L. apetalum and L. perfoliatum possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Our repeat analyses revealed that L. apetalum harboured 20 direct repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas, L. perfoliatum had 15 direct repeats, 20 palindrome repeats, four reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium medicinal plant cp genomes, and a high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments. Codon usage analysis showed that codon 14 was the most frequently used codon in the Lepidium coding sequences. Further, correlation investigations suggest that L. apetalum and L. perfoliatum originate from similar genetic backgrounds. Analysis of codon usage bias of Lepidium cp genome was strongly influenced by mutation and natural selection. We showed that L. apetalum and L. perfoliatum will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.
Keywords: chloroplast genome, codon usage bias, comparative analysis, IR boundary analysis, Lepidium medicinal plants, phylogenetic analysis, repeat sequence, simple sequence repeats (SSR).
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