Abstract
The family Asteraceae includes about 10% of angiosperm species. The tribe Gymnarrheneae is an excellent example of a nonmissing link tribe. It contains two monotypic genera (Cavea and Gymnarrhena) and is positioned phylogenetically to a large clade of Asteroideae + Corymbiodeae + Cichorioideae which contain more than 80% of all the Asteraceae. The genus Cavea (tribe Gymnarrheneae) is a medicinally significant genus and relatively rare in the Qinghai-Tibet Plateau (QTP) and its adjacent areas. Based on the limited evidence, resolving phylogenetic relationship of the genus Cavea has proven difficult for a long time. Despite its important medicinal value, genomic resources of Cavea are still lacking, preventing our understanding of its evolutionary history. In recent years, the plastid genomes are widely used in phylogenetic analysis. To provide more useful genetic data for resolving the systematic disputation of Cavea, here, a complete chloroplast genome of Cavea tanguensis was obtained using Illumina sequencing data for the first time. The whole circular cp genome of C. tanguensis was 150,799 bp in length, contained a large single-copy (LSC) region of 82,514 bp and a small single-copy (SSC) region of 18,471 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them being 24,907 bp in length. A total of 135 functional genes were annotated which consisted of 89 protein-coding genes, 38 trnA genes, and eight rRNA genes. The overall GC content of the chloroplast genome sequence was 37.5%, and the GC contents of the LSC, SSC and IR regions were 35.6%, 30.9% and 37.0%, respectively. We analysed insertions/deletions, and simple-sequence repeats in the chloroplast genomes, and discovered relatively highly variable regions (trnD-GUC/rpoB, trnL-UCC/ndhK, and ycf 1) that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetic studies in Asteraceae. The phylogenetic analyses based on 22 complete chloroplast genome sequences robustly supported that C. tanguensis formed a sister group with the subfamilies Asteroideae and Carduoideae, consistent with the finding of recent studies. This study provides new insight into the plastid genome evolution and phylogenetic relationships. Moreover, it would be fundamental to formulate potential conservation and management strategies for the enigmatic species in the Himalaya.
Similar content being viewed by others
References
Amiryousefi A., Hyvönen J. and Poczai P. 2018 IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34, 3030–3031.
Anderberg A. A. and Ohlson J. L. 2012 The genus Cavea, an addition to the tribe Gymnarrheneae (Asteraceae–Gymnarrhenoideae). Compositae Newslet. 50, 46–55.
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K. et al. 2009 BLAST+: architecture and applications. BMC Bioinformatics 10, 421.
Chen Y. S. and Anderberg A. A. 2011 Cavea W.W. Sm. & Small. In Flora of China (eds. Z. Y. Wu, P. H. Raven and D. Y. Hong), vol. 20, Science Press, Missouri Botanical Garden Press, Beijing, St. Louis.
Dong W., Liu J., Yu J., Wang L. and Zhou S. 2012 Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7, e35071.
Frazer K. A., Pachter L., Poliakov A., Rubin E. M. and Dubchak I. 2004 VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32, W273–W279.
Fu Z. X., Jiao B. H., Nie B., Zhang G. J. and Gao T. G. 2016 A comprehensive generic-level phylogeny of the sunflower family: implications for the systematics of Chinese Asteraceae. J. Syst. Evol. 54, 416e437.
Hall T. A. 1999 BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95–98.
Jansen R. K. and Palmer J. D. 1987 A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84, 5858–5822.
Jeffrey C. 2007 Carduoid genera of uncertain placement. In The families and genera of vascular plants, pp. 146–147. Springer, Berlin and Heidelberg.
Katoh K. and Standley D. M. 2013 MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780.
Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S. et al. 2012 Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.
Librado P. and Rozas J. 2009 DnaSP v5: a Software for Comprehensive Analysis of DNA Polymorphism Data. Bioinformatics 25, 1451–1452.
Lin N., Zhang X., Deng T., Zhang J. W., Meng A. P., Wang H. C. et al. 2019 Plastome sequencing of Myripnois dioica and comparison within Asteraceae. Plant Divers. 41, 315–322.
Ling Y. 1979 Cavea. In Flora reipublicae popular is sinicae (ed. Y. Ling), pp. 4–7. Science Press, Beijing.
Liu Y., Huo N., Dong L., Wang Y., Zhang S., Young H. A. et al. 2013 Complete chloroplastgenome sequences of mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS One 8, e57533.
Lohse M., Drechsel O., Kahlau S. and Bock R. 2013 Organellar genome DRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and vsualizing expression data sets. Nucleic Acids Res. 41, W575–W581.
Mandel J. R., Dikow R. B., Siniscalchi C. M., Thapa R., Watson L. E. and Funk V. A. 2019 A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proc. Natl. Acad. Sci. USA 116, 14083–14088.
Miller M. A., Pfeiffer W. and Schwartz T. 2010 Creating the CIPRES science gateway for inference of large phylogenetic trees. In Proceedings of the Gateway Computing Environments Workshop (GCE) New Orleans, pp. 1–8. IEEE.
Neubig K. M. and Abbott J. R. 2010 Primer development for the plastid region ycf1 in Annonaceae and other magnoliids. Am. J. Bot. 97, e52–e55.
Neubig K. M., Whitten W. M., Carlsward B. S., Blanco M. A., Endara L., Williams N. H. et al. 2009 Phylogenetic utility of ycf 1 in orchids: a plastid gene more variable than matK. Plant Syst. Evol. 277, 75–84.
Panero J. L. and Funk V. A. 2002 Toward a phylogenetic subfamilial classification for the Compositae. P. Biol. Soc. Wash. 115, 909–922.
Panero J. L. and Funk V. A. 2007 New infrafamilial taxa in Asteraceae. Phytologia 89, 356–360.
Panero J. L. and Funk V. A. 2008 The value of sampling anomalous taxa in phylogenetic studies: Major clades of the Asteraceae revealed. Mol. Phylogenet. Evol. 47, 757–782.
Panero J. L. and Funk V. A. 2009 New tribes in Asteraceae. Phytologia 91, 568–570.
Panero J. L., Susana E. F., Espinar L. A., Crozier B. S., Barboza G. E. and Cantero J. J. 2014 Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae. Mol. Phylogenet. Evol. 80, 43–53.
Pelser P. B. and Watson L. E. 2009 Introduction to Asteroideae. In Systematics, evolution, and biogeography of compositae (ed. V. A. Funk, A. Susanna, T. F. Stuessy and R. J. Bayer), pp. 495–502. International Association for Plant Taxonomy (IAPT), Vienna, Austria.
Rozas J., Ferrer-Mata A., Sánchez-DelBarrio J. C., Guirao-Rico S., Librado P., Ramos-Onsins S. E. et al. 2017 DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299–3302.
Schattner P., Brooks A. N. and Lowe T. M. 2005 The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686–W689.
Shen X. F., Wu M., Liao B. S., Liu Z. X., Bai R., Xiao S. M. et al. 2017 Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Molecules 22, 1330.
Shih C., Chen Y. L., Chen Y. S., Lin Y. R., Liu S. W. and Ge X. J. 2011 Asteraceae (Compositae). In Flora of China (ed. Z. Y. Wu, P. H. Raven and D. Y. Hong), pp. 20–21. Science Press, Beijing, St. Louis: Missouri Botanical Garden Press.
Smith W. W. and Small J. 1917 Cavea: A new genus of the Compositae from the East Himalaya. Trans. Proc. Bot. Soc. Edinburgh. 27, 119–123.
Stamatakis A. 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
Tillich M., Lehwark P., Pellizzer T., UlbrichtJones E. S., Fischer A., Bock R. et al. 2017 GeSeq – Versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45, W6–W11.
Wyman S. K., Jansen R. K. and Boore J. L. 2004 Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252–3255.
Zhang X., Deng T., Moore M. J., Ji Y. H., Lin N., Zhang H. J. et al. 2019 Plastome phylogenomics of Saussurea (Asteraceae: Cardueae). BMC Plant Biol. 19, 290.
Acknowledgements
The authors would like to acknowledge Dr Cai-Fei Zhang (Wuhan Botanical Garden, the Chinese Academy of Sciences), Dr Yan-Lei Feng (School of Life Sciences, Westlake University) for providing photo and suggestions. The research was founded by The National Natural Science Foundation of China (32000158), the Special Research Project of National Tradition Chinese Medicine Industy, the Fourth National Survey on Chinese Material Medica Resources (GZY-KJS-2018-004), the Sichuan Science and Technology Research Projects of Traditional Chinese Medicine: (2018PC005), the Project of Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University (2020CXZX03); the Philosophy and Social Science Key Research Base Project of Sichuan Province, Sichuan Nationalities and Mountain Economy Development Research Center (SDJJ1907).
Author information
Authors and Affiliations
Corresponding author
Additional information
Corresponding editor: Rajeev Varshney
Rights and permissions
About this article
Cite this article
YU, S., YANG, X., TIAN, X. et al. The complete chloroplast genome sequence of the monotypic and enigmatic genus Cavea (tribe Gymnarrheneae) and a comparison with other species in Asteraceae. J Genet 101, 20 (2022). https://doi.org/10.1007/s12041-022-01360-3
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12041-022-01360-3