The Complete Chloroplast Genome Sequence of the Medicinal Moss (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Jul 27

PMID 39062679

Authors

Zhengyuan Shen

Qin Liu

Jiewei Hao

Sheng Bi

Yezhen Fu

Lina Zhang

Affiliations

Soon will be listed here.

Abstract

(Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of , including its assembly and annotation. The circular chloroplast genome of is 124,315 bp in length, displaying a typical quadripartite structure with 128 genes: 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Analyses of codon usage bias, repetitive sequences, and simple sequence repeats (SSRs) revealed an A/U-ending codon preference, 96 repetitive sequences, and 385 SSRs in the chloroplast genome. Nucleotide diversity analysis identified 10 high mutational hotspots. Ka/Ks ratio analysis suggested potential positive selection in , , , and genes. Phylogenetic analysis of whole chloroplast genomes from 38 moss species positioned within Bryales, closely related to . This study augments the chloroplast genomic data for Bryales and provides a foundation for molecular marker development and genetic diversity analyses in medicinal bryophytes.

Citing Articles

Characterization of the complete chloroplast genome and development of molecular markers of Salix.

Wang P, Guo J, Zhou J, Wang Y Sci Rep. 2024; 14(1):28528.

PMID: 39557994 PMC: 11574008. DOI: 10.1038/s41598-024-79604-8.

References

Frazer K, Pachter L, Poliakov A, Rubin E, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004; 32(Web Server issue):W273-9. PMC: 441596. DOI: 10.1093/nar/gkh458. View

Bell D, Lin Q, Gerelle W, Joya S, Chang Y, Taylor Z . Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. Am J Bot. 2019; 107(1):91-115. DOI: 10.1002/ajb2.1397. View

Beier S, Thiel T, Munch T, Scholz U, Mascher M . MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017; 33(16):2583-2585. PMC: 5870701. DOI: 10.1093/bioinformatics/btx198. View

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A . Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020; 70(1):e102. DOI: 10.1002/cpbi.102. View

Li S, Shen F, Zhang S, Niu J, Niu Y, Li L . The complete chloroplast genome of (Hampe ex Ochi) Z. Iwatsuki and T. J. Koponen. Mitochondrial DNA B Resour. 2021; 6(9):2632-2634. PMC: 8366662. DOI: 10.1080/23802359.2021.1962759. View

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S . Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647-9. PMC: 3371832. DOI: 10.1093/bioinformatics/bts199. View

Minh B, Schmidt H, Chernomor O, Schrempf D, Woodhams M, von Haeseler A . IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020; 37(5):1530-1534. PMC: 7182206. DOI: 10.1093/molbev/msaa015. View

Yang T, Aishan S, Zhu J, Qin Y, Liu J, Liu H . Chloroplast Genomes and Phylogenetic Analysis of Three (Asteraceae) Species. Int J Mol Sci. 2023; 24(21). PMC: 10648744. DOI: 10.3390/ijms242115634. View

Li X, Yang Y, Henry R, Rossetto M, Wang Y, Chen S . Plant DNA barcoding: from gene to genome. Biol Rev Camb Philos Soc. 2014; 90(1):157-66. DOI: 10.1111/brv.12104. View

10.

He B, Dong H, Jiang C, Cao F, Tao S, Xu L . Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending. Sci Rep. 2016; 6:35927. PMC: 5093902. DOI: 10.1038/srep35927. View

11.

Sharp P, Tuohy T, Mosurski K . Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986; 14(13):5125-43. PMC: 311530. DOI: 10.1093/nar/14.13.5125. View

12.

Rozas J, Ferrer-Mata A, Sanchez-DelBarrio J, Guirao-Rico S, Librado P, Ramos-Onsins S . DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol. 2017; 34(12):3299-3302. DOI: 10.1093/molbev/msx248. View

13.

Zhou X, Peng T, Zeng Y, Cai Y, Zuo Q, Zhang L . Chromosome-level genome assembly of provides new insights into heat stress responses in mosses. Front Plant Sci. 2023; 14:1271357. PMC: 10619864. DOI: 10.3389/fpls.2023.1271357. View

14.

Boetzer M, Henkel C, Jansen H, Butler D, Pirovano W . Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2010; 27(4):578-9. DOI: 10.1093/bioinformatics/btq683. View

15.

Chen J, Wang F, Zhao Z, Li M, Liu Z, Peng D . Complete Chloroplast Genomes and Comparative Analyses of Three (Aeridinae, Orchidaceae) Species. Int J Mol Sci. 2023; 24(13). PMC: 10342943. DOI: 10.3390/ijms241311167. View

16.

Wang D, Zhang Y, Zhang Z, Zhu J, Yu J . KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010; 8(1):77-80. PMC: 5054116. DOI: 10.1016/S1672-0229(10)60008-3. View

17.

Horwath A, Royles J, Tito R, Gudino J, Allen N, Farfan-Rios W . Bryophyte stable isotope composition, diversity and biomass define tropical montane cloud forest extent. Proc Biol Sci. 2019; 286(1895):20182284. PMC: 6364587. DOI: 10.1098/rspb.2018.2284. View

18.

Yang Z, Nielsen R . Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000; 17(1):32-43. DOI: 10.1093/oxfordjournals.molbev.a026236. View

19.

Lin X, Lee S, Ni J, Zhang X, Hu X, Zou P . Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in . Int J Mol Sci. 2023; 24(20). PMC: 10607086. DOI: 10.3390/ijms242015138. View

20.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View