Complete Chloroplast Genome Sequence of Adenophora Racemosa (Campanulaceae): Comparative Analysis with Congeneric Species

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2021 Mar 18

PMID 33735287

Citations 9

Authors

Kyung-Ah Kim

Kyeong-Sik Cheon

Affiliations

Soon will be listed here.

Abstract

Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

Citing Articles

Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus L.

Tussipkan D, Shevtsov V, Ramazanova M, Rakhimzhanova A, Shevtsov A, Manabayeva S Front Plant Sci. 2024; 15:1433253.

PMID: 39600902 PMC: 11588485. DOI: 10.3389/fpls.2024.1433253.

Characterization of the complete chloroplast genome of Rhodiola sachalinensis and comparative analysis with its congeneric plants.

Sun T, Tang Y, Zhou L, Qiao X, Ma X, Qin H FEBS Open Bio. 2024; 14(8):1340-1355.

PMID: 38965647 PMC: 11301261. DOI: 10.1002/2211-5463.13854.

Comparative Plastid Genome and Phylogenomic Analyses of Species.

Choi K, Hwang Y, Hong J, Kang J Genes (Basel). 2023; 14(10).

PMID: 37895263 PMC: 10606940. DOI: 10.3390/genes14101914.

The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships.

An S, Kim B, Kang H, Lee H, Lee Y, Park Y PLoS One. 2023; 18(10):e0292056.

PMID: 37815995 PMC: 10564136. DOI: 10.1371/journal.pone.0292056.

The First Complete Chloroplast Genome of : Genome Characterization and Phylogenetic Diversity.

Yoon W, Kim C, Kim Y Genes (Basel). 2023; 14(8).

PMID: 37628648 PMC: 10454809. DOI: 10.3390/genes14081597.

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

Marcussen T, S Meseguer A . Species-level phylogeny, fruit evolution and diversification history of Geranium (Geraniaceae). Mol Phylogenet Evol. 2017; 110:134-149. DOI: 10.1016/j.ympev.2017.03.012. View

Cho K, Yun B, Yoon Y, Hong S, Mekapogu M, Kim K . Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum). PLoS One. 2015; 10(5):e0125332. PMC: 4428892. DOI: 10.1371/journal.pone.0125332. View

Cheon K, Kim K, Yoo K . The complete chloroplast genome sequences of three Adenophora species and comparative analysis with Campanuloid species (Campanulaceae). PLoS One. 2017; 12(8):e0183652. PMC: 5568750. DOI: 10.1371/journal.pone.0183652. View

Wyman S, Jansen R, Boore J . Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004; 20(17):3252-5. DOI: 10.1093/bioinformatics/bth352. View

Lohse M, Drechsel O, Bock R . OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 2007; 52(5-6):267-74. DOI: 10.1007/s00294-007-0161-y. View

Weng M, Blazier J, Govindu M, Jansen R . Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol. 2013; 31(3):645-59. DOI: 10.1093/molbev/mst257. View

Tu P, Niu Y, Xu L, Xu G . [Microscopic identification of the powder of roots of genus Adenophora: II. The roots of Sect. Remotiflorae and Sect. Adenophora]. Zhongguo Zhong Yao Za Zhi. 1997; 22(2):67-72, 126. View

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

10.

Cosner M, Raubeson L, Jansen R . Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol Biol. 2004; 4:27. PMC: 516026. DOI: 10.1186/1471-2148-4-27. View

11.

Souza U, Nunes R, Targueta C, Diniz-Filho J, Telles M . The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species. Sci Rep. 2019; 9(1):14206. PMC: 6775074. DOI: 10.1038/s41598-019-50620-3. View

12.

Schattner P, Brooks A, Lowe T . The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005; 33(Web Server issue):W686-9. PMC: 1160127. DOI: 10.1093/nar/gki366. View

13.

Cheon K, Yoo K . Complete chloroplast genome sequence of Hanabusaya asiatica (Campanulaceae), an endemic genus to Korea. Mitochondrial DNA A DNA Mapp Seq Anal. 2014; 27(3):1629-31. DOI: 10.3109/19401736.2014.958702. View

14.

Darriba D, Taboada G, Doallo R, Posada D . jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012; 9(8):772. PMC: 4594756. DOI: 10.1038/nmeth.2109. View

15.

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

16.

Haberle R, Fourcade H, Boore J, Jansen R . Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol. 2008; 66(4):350-61. DOI: 10.1007/s00239-008-9086-4. View

17.

Hong C, Park J, Lee Y, Lee M, Park S, Uhm Y . accD nuclear transfer of Platycodon grandiflorum and the plastid of early Campanulaceae. BMC Genomics. 2017; 18(1):607. PMC: 5553655. DOI: 10.1186/s12864-017-4014-x. View

18.

Yoo K, Cheon K, Kim K . Complete chloroplast genome sequence of Lam. (Campanulaceae). Mitochondrial DNA B Resour. 2021; 1(1):184-185. PMC: 7871831. DOI: 10.1080/23802359.2016.1149791. View

19.

Tu P, Niu Y, Xu L, Xu G . [Microscopic identification of the powder of roots of genus Adenophora. I. The roots of Sect. Basiphyllae and Sect. Pachydiscus]. Zhongguo Zhong Yao Za Zhi. 1996; 21(10):581-5, 639. View

20.

Guisinger M, Kuehl J, Boore J, Jansen R . Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc Natl Acad Sci U S A. 2008; 105(47):18424-9. PMC: 2587588. DOI: 10.1073/pnas.0806759105. View