Complete Chloroplast Genome Sequence of and Comparative Analysis of the Malvaceae Family

Overview

Journal Front Genet

Date 2020 Apr 8

PMID 32256523

Citations 21

Authors

Yan Cheng

Liemei Zhang

Jianmin Qi

Liwu Zhang

Affiliations

Soon will be listed here.

Abstract

Kenaf () is one of the most fast-growing bast in the world and belongs to the family Malvaceae. However, the systematic classification and chloroplast (cp) genome of kenaf has not been reported to date. In this study, we sequenced the cp genome of kenaf and conducted phylogenetic and comparative analyses in the family of Malvaceae. The sizes of cp genomes were 162,903 bp in length, containing 113 unique genes (79 protein-coding genes, four rRNA genes, and 30 tRNA genes). Phylogenetic analysis indicated that the cp genome sequence of has closer relationships with and than with , which disagrees with the taxonomical relationship. Further analysis obtained a new version of the cp genome annotation of and found that the orientation variation of small single copy (SSC) region exists widely in the family of Malvaceae. The highly variable and the highly conserved gene were identified among the family of Malvaceae. In particular, the explanation for two different SSC orientations in the cp genomes associated with phylogenetic analysis is discussed. These results provide insights into the systematic classification of the genus in the Malvaceae family.

Citing Articles

Comparative analyses of chloroplast genomes of Theobroma cacao from northern Peru.

Tineo D, Bustamante D, Calderon M, Oliva M PLoS One. 2025; 20(3):e0316148.

PMID: 40043011 PMC: 11882073. DOI: 10.1371/journal.pone.0316148.

Revisiting Phryma leptostachya L.: phylogenetic relationships and biogeographical patterns from complete plastome.

Kim Y, Jeong S, Park I, Moon H BMC Plant Biol. 2025; 25(1):278.

PMID: 40033209 PMC: 11877724. DOI: 10.1186/s12870-025-06272-9.

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.

Repeat-mediated recombination results in Complex DNA structure of the mitochondrial genome of Trachelospermum jasminoides.

Cai Y, Chen H, Ni Y, Li J, Zhang J, Liu C BMC Plant Biol. 2024; 24(1):966.

PMID: 39407117 PMC: 11481363. DOI: 10.1186/s12870-024-05568-6.

Characterization of the Plastid Genomes of Four Thunb. Species from Kazakhstan.

Almerekova S, Yermagambetova M, Osmonali B, Vesselova P, Abugalieva S, Turuspekov Y Plants (Basel). 2024; 13(10).

PMID: 38794403 PMC: 11124919. DOI: 10.3390/plants13101332.

References

Librado P, Rozas J . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25(11):1451-2. DOI: 10.1093/bioinformatics/btp187. View

Daniell H, Lin C, Yu M, Chang W . Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016; 17(1):134. PMC: 4918201. DOI: 10.1186/s13059-016-1004-2. View

Mustardy L, Buttle K, Steinbach G, Garab G . The three-dimensional network of the thylakoid membranes in plants: quasihelical model of the granum-stroma assembly. Plant Cell. 2008; 20(10):2552-7. PMC: 2590735. DOI: 10.1105/tpc.108.059147. View

Schattat M, Barton K, Baudisch B, Klosgen R, Mathur J . Plastid stromule branching coincides with contiguous endoplasmic reticulum dynamics. Plant Physiol. 2011; 155(4):1667-77. PMC: 3091094. DOI: 10.1104/pp.110.170480. View

Dong W, Xu C, Cheng T, Zhou S . Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales. PLoS One. 2013; 8(10):e77965. PMC: 3799696. DOI: 10.1371/journal.pone.0077965. View

Jagendorf A, Uribe E . ATP formation caused by acid-base transition of spinach chloroplasts. Proc Natl Acad Sci U S A. 1966; 55(1):170-7. PMC: 285771. DOI: 10.1073/pnas.55.1.170. 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

Xu Q, Xiong G, Li P, He F, Huang Y, Wang K . Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids. PLoS One. 2012; 7(8):e37128. PMC: 3411646. DOI: 10.1371/journal.pone.0037128. View

Dong W, Xu C, Cheng T, Lin K, Zhou S . Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of saxifragales. Genome Biol Evol. 2013; 5(5):989-97. PMC: 3673619. DOI: 10.1093/gbe/evt063. View

10.

Huang H, Shi C, Liu Y, Mao S, Gao L . Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol. 2014; 14:151. PMC: 4105164. DOI: 10.1186/1471-2148-14-151. View

11.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

12.

Kumar S, Stecher G, Tamura K . MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016; 33(7):1870-4. PMC: 8210823. DOI: 10.1093/molbev/msw054. View

13.

Nazareno A, Carlsen M, Lohmann L . Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PLoS One. 2015; 10(6):e0129930. PMC: 4478014. DOI: 10.1371/journal.pone.0129930. View

14.

Zhang L, Li A, Wang X, Xu J, Zhang G, Su J . Genetic diversity of kenaf (Hibiscus cannabinus) evaluated by inter-simple sequence repeat (ISSR). Biochem Genet. 2013; 51(9-10):800-10. DOI: 10.1007/s10528-013-9608-7. View

15.

Tamura K, Nei M, Kumar S . Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004; 101(30):11030-5. PMC: 491989. DOI: 10.1073/pnas.0404206101. View

16.

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

17.

Jin S, Daniell H . The Engineered Chloroplast Genome Just Got Smarter. Trends Plant Sci. 2015; 20(10):622-640. PMC: 4606472. DOI: 10.1016/j.tplants.2015.07.004. View

18.

Lohse M, Drechsel O, Kahlau S, Bock R . OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013; 41(Web Server issue):W575-81. PMC: 3692101. DOI: 10.1093/nar/gkt289. View

19.

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

20.

Shen X, Wu M, Liao B, Liu Z, Bai R, Xiao S . Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. Molecules. 2017; 22(8). PMC: 6152406. DOI: 10.3390/molecules22081330. View