Characterization of the complete chloroplast genome of Pedicularis flava (Orobanchaceae)
UDC 582.952.6+575.113
Keywords:
flora of Mongolia, Pedicularis, phylogeny, plastome, whole genome
Abstract
Pedicularis flava Pall. is perennial herb and is distributed in China (Inner Mongolia), Mongolia and Russia (Zabaikalye Territory – Chita city, Republic of Tyva). In Mongolia, this species is quite widely distributed across several phytogeographical regions. In this study, we assembled and annotated the complete plastid genome of P. flava using the high-through sequencing for the first time. The plastome of P. flava was identified as a double-stranded circular DNA molecule 149 087 bp long with 38.4 % GC content. The plastome consists of a large single-copy (LSC) region (83 576 bp) and a small single-copy (SSC) region (14 169 bp) and separated by two inverted repeats (IRs) of 25 671 bp each. The plastome encodes 113 unique genes which is similar to other Pedicularis species. This includes 4 rRNA, 30 tRNA, and 79 protein-coding genes, among which 4 rRNA, 7 tRNA, and 7 protein-coding genes were duplicated in the IR regions. Finally, phylogenetic analysis shows that Pedicularis species were formed a monophyletic clade and P. flava was clustered with P. resupinata.
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References
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Baasanmunkh S., Urgamal M., Oyuntsetseg B., Sukhorukov A. P., Tsegmed Z., Son D. C., et al. 2022. Flora of Mongolia: annotated checklist of native vascular plants. PhytoKeys 192: 63–169. https://doi.org/10.3897/phytokeys.192.79702
Beier S., Thiel T., Münch T., Scholz U., Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16): 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Bolger A. M., Lohse M., Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15): 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Cho W. B., Choi B. H., Kim J. H., Lee D. H., Lee J. H. 2018. Complete plastome sequencing reveals an extremely diminished SSC region in hemiparasitic Pedicularis ishidoyana (Orobanchaceae). Ann. Bot. Fenn. 55: 171–183. https://doi.org/10.5735/085.055.0122
Dierckxsens N., Mardulyn P., Smits G. 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucl. Acids Res. 45(4): gkw955. https://doi.org/10.1093/nar/gkw955
Doyle J. J., Doyle J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull. 19: 11–15.
Gao L. Z., Liu Y. L., Zhang D., Li W., Gao J., Liu Y., Li K., Shi C., Zhao Y., Zhao Y. J., Jiao J. Y. 2019. Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats. Commun. Biol. 2(1): 278. https://doi.org/10.1038/s42003 019 0531 2
Jiang Y., Li H., Wu M., Zhang X., Baasanmukh S., Li H., Sun H., Chen S. 2025. Comparative chloroplast genomes of Incarvillea species (Bignoniaceae) unveiled genomic diversity and shed light on phylogenetic relationships. BMC Plant Biol. 25: 399. https://doi.org/10.1186/s12870-025-06380-6
Katoh K. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14): 3059–3066. https://doi.org/10.1093/nar/gkf436
Kosachev P. A. 2010. Synopsis of the families Scrophulariaceae Juss. and Pediculariaceae Juss. of Altai mountain country. Turczaninowia 13, 1: 19–102.
Kusnetsov V. V. 2018. Chloroplasts: Structure and expression of the plastid genome. Rus. J. Plant Physiol. 65: 465–476. https://doi.org/10.1134/S1021443718030044
Li X., Yang J.-B., Wang H., Song Y., Corlett R. T., Yao X., Li D.-Z., Yu W.-B. 2021. Plastid NDH pseudogenization and gene loss in a recently derived lineage from the largest hemiparasitic plant genus Pedicularis (Orobanchaceae). Plant Cell Physiol. 62(6): 971–984. https://doi.org/10.1093/pcp/pcab074
Liu M.-L., Yu W.-B., Wang H. 2013. Rapid identification of plant species and iFlora: Application of DNA barcoding in a large temperate genus Pedicularis (Orobanchaceae). Plant Divers. 35(6): 707–714. https://doi.org/10.7677/ynzwyj201313168
Liu S., Ni Y., Li J., Zhang X., Yang H., Chen H., Liu C. 2023. CPGView: A package for visualizing detailed chloroplast genome structures. Mol. Ecol. Res. 23(3): 694–704. https://doi.org/10.1111/1755-0998.13729
Nyamgerel N., Baasanmunkh S., Oyuntsetseg B., Bayarmaa G.-A., Erst A., Park I., Choi H. J. 2023. Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe. Sci. Rep. 13: 1–12. https://doi.org/10.1038/s41598-023-49381-x
Oyuntsetseg D., Nyamgerel N., Baasanmunkh S., Oyuntsetseg B., Urgamal M., Yoon J. W., Bayarmaa G.-A., Choi H. J. 2024. The complete chloroplast genome and phylogenetic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia. Bot. Stud. 65: 11. https://doi.org/10.1186/s40529-024-00417-z
POWO [2024]. Plants of the World Online. Kew: Facilitated by the Royal Botanic Gardens. URL: http://www.plantsoftheworldonline.org (Accessed 16 November 2024).
Provan J., Powell W., Hollingsworth P. M. 2001. Chloroplast microsatellites: New tools for studies in plant ecology and evolution. Trends Ecol. Evol. 16(3): 142–147. https://doi.org/10.1016/S0169-5347(00)02097-8
Rambaut A. 2012. FigTree v1. 4. Molecular evolution, phylogenetics and epidemiology. Edinburgh: University of Edinburgh, Institute of Evolutionary Biology.
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9): 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Tamura K., Stecher G., Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 38(7): 3022–3027. https://doi.org/10.1093/molbev/msab120
Tillich M., Lehwark P., Pellizzer T., Ulbricht-Jones E. S., Fischer A., Bock R., Greiner S. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucl. Acids Res. 45(W1): W6–W11. https://doi.org/10.1093/nar/gkx391
Tkach N., Ree R. H., Kuss P., Röser M., Hoffmann M. H. 2014. High mountain origin, phylogenetics, evolution, and niche conservatism of arctic lineages in the hemiparasitic genus Pedicularis (Orobanchaceae). Mol. Phylogenetics Evol. 76: 75–92. https://doi.org/10.1016/j.ympev.2014.03.004
Wang M., Zhang S., Zhang L. 2024. The complete chloroplast genome sequences of three Pedicularis species (Orobanchaceae). Genet. Mol. Biol. 47(3): e20240010. https://doi.org/10.1590/1678-4685-GMB-2024-0010
Wang T., Li X., Tang C., Cao Z., He H., Ma X., Li Y., De K. 2024. Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis. Sci. Rep. 14: 14357. https://doi.org/10.1038/s41598-024-63815-0
Wu C., Fang D., Wei J., Wang X., Chen X. 2019. The complete chloroplast genome of Pedicularis alaschanica (Orobanchaceae). Mitochondrial DNA 4(2): 2197–2198. https://doi.org/10.1080/23802359.2019.1623723
Yu W.-B., Huang P.-H., Ree R. H., Liu M.-L., Li D.-Z., Wang H. 2011. DNA barcoding of Pedicularis L. (Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus. J. Syst. Evol. 49(5): 425–437. https://doi.org/10.1111/j.1759-6831.2011.00154.x
Zhang R., Wang J., Han K., Ting R., Shuyun Z., Edward B., Zhan-Lin L. 2017. Complete chloroplast genome sequence of Pedicularis cheilanthifolia, an alpine plant in China. Conserv. Genet. Resour. 9: 619–621. https://doi.org/10.1007/s12686-017-0740-2
Zhang Q., Lu Z., Guo M., Kang J., Li J., He X., Wu J., Liu R., Dang J., Li Z. 2024. Responses of three Pedicularis species to geological and climatic changes in the Qinling Mountains and adjacent areas in East Asia. Plants 13: 765. https://doi.org/10.3390/plants13060765
Published
2025-06-30
How to Cite
Baasanmunkh S., Nyamgerel N., Munkhtulga D., Oyuntsetseg B., Bayarmaa G.-A., Kubentayev S. A., Tsegmed Z., Choi H. J. Characterization of the complete chloroplast genome of Pedicularis flava (Orobanchaceae) // Turczaninowia, 2025. Vol. 28, № 2. P. 112-120 DOI: 10.14258/turczaninowia.28.2.11. URL: https://turczaninowia.asu.ru/article/view/17514.
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