TSitologiya i Genetika 2023, vol. 57, no. 2, 58-61
Cytology and Genetics 2023, vol. 57, no. 2, 174–185, doi: https://www.doi.org/10.3103/S0095452723020081

Molecular organization of the chloroplast genome and taxonomic position of Stellaria dichotoma var. lanceolate

Liu W., Qiu K., Huang Y., Li Y., Zhang S.

  1. School of Agriculture, Ningxia University, Yinchuan, Ningxia, China
  2. Ningxia Grassland and Animal Husbandry Engineering Technology, Research Center, Yinchuan, Ningxia, China
  3. Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China

Stellaria dichotoma L. var. lanceolata Bunge is a typical rare medicinal plant commonly used in therapeutic formulations. To reveal the structural arrangents and variation of complete chloroplast genomes between S. dichotoma var. lanceolata and its related species is of great significance for the study of its evolutionary status. In this study, evolutionary relationships between S. dichotoma var. lanceolata and its related species of Caryophyllaceae were documented based on the complete chloroplast genome sequence of S. dichotoma var. lanceolata. The result showed that the whole circular genome of S. dichotoma var. lanceolata was 150,461 bp in length, annotated 129 genes, possessing RSCU of 21 types of amino acids and 64 codons encoding. By comparing and analyzing the SSR and variation region of the chloroplast gene of S. dichotoma var. lanceolata and its related genus pseudostellaria, we found that the divergent regions of trnk­rps16, atpH­atpI, rpoC1­rpoB, rbcL­accD, trnS­trnG, psaA­ycf3, trnV­trnM, ycf4­cemA, petL­petG, trnL­ccsA, ndhF, ndhA, and ycf1 fragments were highly obvious, which could be used as DNA barcodes for the taxonomic evidence of S. dichotoma var. Lanceolata and Pseudostellaria in Caryophyllaceae. A maximum likelihood (ML) phylogenetic tree elucidated that S. dichotoma var. lanceolata was closely related to pseudostellaria, and cluster into a branch with Cerastium. Our results lay a robust foundation for future phylogenetic and evolutionary status of S. dichotoma var. lanceolata and among relatives within Caryophyllaceae.

Keywords: Complete chloroplast genome; Stellaria dicho­toma var. lanceolata; Caryophyllaceae; Pseudostellaria; phylogenetic analysis

TSitologiya i Genetika
2023, vol. 57, no. 2, 58-61

Current Issue
Cytology and Genetics
2023, vol. 57, no. 2, 174–185,
doi: 10.3103/S0095452723020081

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Altschul, S.F., Madden, T.L., Schäffer A.A., Zhang, J.H., Zhang, Z., Miller, W., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, vol. 25, pp. 3389–3402. https://doi.org/10.1093/nar/25.17.3389

Alzahrani, D.A., Complete chloroplast genome of Abutilon fruticosum: Genome structure, comparative and phylogenetic analysis, Plants (Basel), 2021, vol. 10, no. 2, pp. 270. https://doi.org/10.3390/PLANTS10020270

Amiryousefi, A., Hyvonen, J., and Poczai, P., IRscope: an online program to visualize the junction sites of chloroplast genomes, Bioinformatics, 2018, vol. 34, pp. 3030–3031. https://doi.org/10.1093/bioinformatics/bty220

Androsiuk, P., Jastrzebski, J.P., Paukszto, T., Makowczenko, K., Okouski, A., Pszczotkowska, A., et al., Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species, Sci. Rep., 2018, vol. 10, pp. 11522. https://doi.org/10.1038/s41598-020-68563-5

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol., 2012, vol. 19, no. 5, pp. 455–477. https://https://doi.org/10.1089/cmb.2012.0021

Beier S., Thiel T., Münch T., Scholz U., Mascher M. MISA-web: a web server for microsatellite prediction, Bioinformatics, 2017, vol. 33, pp. 2583–2585. https://doi.org/10.1093/bioinformatics/btx198

Benson, G., Tandem repeats finder: A program to analyze DNA sequences, Nucleic Acids Res., 1999, vol. 27, pp. 573–580. https://doi.org/10.1093/nar/27.2.573

Byng, J.W., Chase, M.W., Christenhusz, M.J., Fay, M.F., Judd, W.S., Mabberley, D.J., et al., An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV, Bot. J. Linn. Soc., 2016, vol. 181, pp. 1–20. https://doi.org/10.1111/boj.12385

Chen, Y.F., Kuo, P.C., Chan, H.H., Kuo, I.J., Lin, F.W., Su, C.R., et al., β-Carboline alkaloids from Stellaria dichotoma var. lanceolate and their anti-inflammatory activity, J. Nat. Prod., 2010, vol. 73, pp. 1993–1998. https://ir.cmu.edu.tw/ir/handle/310903500/42285

Chen, X.B., Meng, S.Y., Zhang, X.F., Han, Y.B., and Liu, Q.R., Numerical taxonomic analysis of Stellaria and Pseudostellaria (Caryophyllaceae), Chin. Bull. Bot., 2014, vol. 49, no. 4, pp. 432–439. https://doi.org/10.3724/SP.J.1259.2014.00432

Cui, N., Liao, B.S., Liang, C.L., Li, S.F., Zhang, H., Xu, J., et al., Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis, Chin. J. Nat. Med., 2020, vol. 18, no. 08, pp. 563–572. https://doi.org/10.1016/S1875-5364(20)30068-6

Dong, W.P., Liu, H., Xu, C., Zuo, Y.J., Chen, Z.J., and Zhou, S.L., A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs, BMC Genet., 2014, vol. 15, p. 138. https://doi.org/10.1186/s12863-014-0138-z

Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M., and Dubchak, I., VISTA: Computational tools for comparative genomics, Nucleic Acids Res., 2004, vol. 32, pp. W273–279. https://doi.org/10.1093/nar/gkh458

Gao, C.W., Wu, C.H., Zhang, Q., Zhao, X., Wu, M.X., Chen, R.R., et al., Characterization of chloroplast genomes from two Salvia medicinal plants and gene transfer among their mitochondrial and chloroplast genomes, Front. Genet., 2020, vol. 11, p. 574962. https://doi.org/10.3389/fgene.2020.574962

Greiner, S., Lehwark, P., and Bock, R., Organellar Genome DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes, Nucleic Acids Res., 2019, vol. 47, pp. W59–W64. https://doi.org/10.1093/nar/gkz238

Guo, M., Xu, Y., Ren, L., He, S., and Pang, A.X., A systematic study on DNA barcoding of medicinally important genus Epimedium L. (Berberidaceae), Genes, 2018, vol. 9, no. 12, p. 637. https://doi.org/10.3390/genes9120637

Hollingsworth, P.M., Li, D.Z., Twyford, B.M., and Twyford, A.D., Telling plant species apart with DNA: from barcodes to genomes, Philos. Trans. R. Soc., B, 2016, vol. 371, no. 1702, p. 201503. https://doi.org/10.1098/rstb.2015.0338

Jansen, R.K., Raubeson, L.A., Boore, J.L., de Pamphilis, C.W., Chumley, T.W., Haberle, R.C., et al., Methods for obtaining and analyzing whole chloroplast genome sequences, Methods Enzymol., 2005, vol. 395, pp. 348–384. https://doi.org/10.1016/S0076-6879(05)95020-9

Katoh, K. and Standley, D.M., MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 2013, vol. 30, pp. 772–780. https://doi.org/10.1093/molbev/mst010

Kučera, J., Svitok, M., Gbúrová, Š.E., Mártonfiová, L., Lafon, P.C., and Slovák, M., Eunuchs or females? Causes and consequences of gynodioecy on morphology, ploidy, and ecology of Stellaria graminea L. (Caryophyllaceae), Front. Plant Sci., 2021, vol. 12, p. 589093. https://doi.org/10.3389/FPLS.2021.589093

Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K., MEGA X: Molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://https://doi.org/10.1093/molbev/msy096

Li, J., Li, H.Y., Zhi, J.K., Shen, C.Z., Yang X.S., and Xu, J.C., Codon usage of expansin genes in Populus trichocarpa, Curr. Bioinf., 2017, vol. 12, no. 5, pp. 452–461. https://doi.org/10.2174/1574893611666161008195145

Li, Z.K., Song, L., Lei, Y., Liang, W.L., Wang, H., and Peng, L., Advances in biology, chemical constituents and pharmacological activities of Stellaria dichotoma var. Lanceolata (in Chinese), J. Nanjing Univ. Tradit. Chin. Med., 2020a, vol. 36, no. 1, pp. 136–140. https://doi.org/10.14148/j.issn.1672-0482.2020.0136

Li, P., Yu, P., and Xia, J., Characterization of the complete chloroplast genome of Stellaria dichotoma var. lanceolata Bunge, a traditional Chinese medicinal plant, Mitochondrial DNA, Part B, 2020b, vol. 5, no. 4, pp. 3848–3850. https://doi.org/10.1080/23802359.2020.1841578

Li, B., Lin, F.R., Huang, P., Guo, W.Y., and Zheng, Y.Q., Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinensegermplasm based on low-coverage whole genome sequencing, Biol. Res., 2020c, vol. 53, no. 6119, pp. e460–e464. https://doi.org/10.1186/s40659-020-00289-0

Luo, K., Ma, P., Song, J.Y., Chen, K.L., and Liu, Y.M., Molecular identifcation of Fritillariae Cirrhosae Bulbus and its adulterants, World Sci. Technol. Modern. Tradit. Chin. Med. Materia Medica, 2012, vol. 14, pp. 1153–1158. https://doi.org/10.11842/wst.2012.1

Luo, C., Li, Y., Budhathoki, R., Shi, J., Yer, H., Li, X., et al., Complete chloroplast genomes of Impatiens cyanantha and Impatiens monticola: Insights into genome structures, mutational hotspots, comparative and phylogenetic analysis with its congeneric species, PloS One, 2021, vol. 16, no. 4, p. e0248182. https://doi.org/10.1371/JOURNAL.PONE.0248182

Maheswari, P., Kunhikannan, C., and Yasodha, R., Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f), J. Biosci., 2021, vol. 46, no. 2, p. 43. https://doi.org/10.1007/S12038-021-00166-2

Mishra, P., Kumar, A., Nagireddy, A., Mani, D.N., Shukla, A.K., Tiwari, R., et al., DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market, Plant Biotechnol. J., 2015, vol. 14, pp. 8–21. https://doi.org/10.1111/pbi.12419

National Pharmacopoeia Committee. Pharmacopoeia of the People’s Republic of China, Beijing: China Med. Sci. Technol. Press, 2015.

Njuguna, A.W., Li, Z.Z., Saina, J.K., Munywoki, J.M., Gichira, A.W., Gituru, R.W., et al., Comparative analyses of the complete chloroplast genomes of Nymphoides and Menyanthes species (menyanthaceae), Aquat. Bot., 2019, vol. 156, pp. 73–81. https://doi.org/10.1016/j.aquabot.2019.05.001

Park, I., Yang, S., Song, J.H., and Moon, B.C., Dissection for floral micromorphology and plastid genome of valuable medicinal borages Arnebia and Lithospermum (Boraginaceae), Front. Plant Sci., 2020, vol. 11, p. 606463. https://doi.org/10.3389/FPLS.2020.606463

Parks, M., Cronn, R., and Liston, A., Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes, BMC Biol., 2009, vol. 7, p. 84. https://doi.org/10.1186/1741-7007-7-84

Peng, J., Zhao, Y.L., Dong, M., Liu, S.Q., Hu, Z.Y., Zhong, X.F., et al., Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes, BMC Ecol. Evol., 2021, vol. 21, no. 1, pp. 71–71. https://doi.org/10.1186/S12862-021-01800-1

Rozas, J., Ferrermata, A., Sánchezdelbarrio, J.C., Guiraorico, S., Librado, P., Ramosonsins, S.E., and Sánchezgracia, A., DnaSP6: DNA sequence polymorphism analysis of large datasets, Mol. Biol. Evol., 2017, vol. 34, pp. 3299–3302. https://doi.org/10.1093/molbev/msx248

Sharples, M.T., Taxonomic observations within Stellaria (Caryophyllaceae): Insights from ecology, geography, morphology, and phylogeny suggest widespread parallelism in starworts and erode previous infrageneric classifications, Syst. Bot., 2019, vol. 44, no. 4, pp. 877–886. https://doi.org/10.1600/036364419X15710776741459

Sharples, M.T. and Tripp, E.A., Phylogenetic relationships within and delimitation of the cosmopolitan flowering plant genus Stellaria L. (Caryophyllaceae): Core stars and fallen stars, Syst. Bot., 2019, vol. 44, no. 4, pp. 857–876. https://doi.org/10.1600/036364419X15710776741440

Sharples, M.T., Bentz, P.C., and Manzitto-Tripp, E.A., Evolution of apetaly in the cosmopolitan genus Stellaria, Am. J. Bot., 2021, vol. 108, no. 5, pp. 869–882. https://doi.org/10.1002/AJB2.1650

Stefanova, P., Taseva, M., Georgieva, T., Gotcheva, V., and Angelov, A., A modified CTAB method for DNA extraction from soybean and meat products, Biotechnol. Biotechnol. Equip., 2013, vol. 27, no. 3, pp. 3803–3810. https://doi.org/10.5504/BBEQ.2013.0026

Van Do, T., Xu, B., and Gao, X.F., Molecular phylogeny and character evolution of Flemingia (Leguminosae, Papilionoideae, Phaseoleae, Cajaninae) inferred from three cpDNA and nrITS sequence data, Plant Syst. Evol., 2021, vol. 307, p. 30. https://doi.org/10.1007/S00606-021-01749-0

Wei, L. and De Craene, L.R., What is the nature of petals in Caryophyllaceae? Developmental evidence clarifies their evolutionary origin, Ann. Bot., 2019, vol. 124, pp. 1–15. https://doi.org/10.1093/aob/mcz075

Wei, F., Tang, D.F., Wei, K.H., Qin, F., Li, L.X., Lin, Y., et al., The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis, Sci. Rep., 2020, vol. 10, p. 12473. https://doi.org/10.1038/s41598-020-69549-z

Wyman, S.K., Jansen, R.K., and Boore, J.L., Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 2004, vol. 20, pp. 3252–3255.

Xu, C., Dong, W., Li, W., Lu, Y., Xie, X., Jin, X., et al., Comparative analysis of six Lagerstroemiacomplete chloroplast genomes, Front. Plant Sci., 2017, vol. 8, p. 15. https://doi.org/10.1093/bioinformatics/bth352

Yang, H.S., Li, X.P., Liu, D.J., Chen, X.B., Li, F.H., Qi, X.L., et al., Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers, Biochem. Systemat. Ecol., 2016, vol. 66, pp. 286–292. https://doi.org/10.1016/j.bse.2016.04.018

Zalapa, J.E., Cuevas, H., Zhu, H., Steffan, S., Senalik, D., Zeldin, E., et al., Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences, Am. J. Bot., 2012, vol. 99, pp. 193–208. https://doi.org/10.3732/ajb.1100394

Zhang, W.J., Cao, Z., Xie, Z.C., Lang, D.Y., Zhou, L., Chu, Y.K., et al., Effect of water stress on roots biomass and secondary metabolites in the medicinal plant Stellaria dichotoma L. var. lanceolata Bge, Scientia Horticulturae, 2017, vol. 224, pp. 280–285. https://doi.org/10.1016/j.scienta.2017.06.030

Zhang, Y., Wang, Z.F., Guo, Y.N., Chen, S., Xu, X.Y., and Wang, R.J., Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships, Gene, 2021, vol. 791, p. 145715. https://doi.org/10.1016/J.GENE.2021.145715

Zheng, G., Wei, L.L., Ma, L., Wu, Z.Q., Gu, C.H., and Chen, K., Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships, Plant Mol. Biol., 2020, vol. 102, no. 6, pp. 659–676. https://doi.org/10.1007/S11103-020-00972-6

Zhou, L., Lang, D.Y., Zhang, W.J., Wang, J.H., Gao, X.J., Wu, X.L., et al., Physiological mechanisms of salt and drought-induced stress effects on root biomass and secondary metabolites in Stellaria dichotoma, Int. J. Agric. Biol., 2019, vol. 22, pp. 1285–1292. https://doi.org/10.17957/IJAB/15.1200

Zhu, S., Liu, Q.D., He, J.Y., Nakajima, N., Samarako-on, S.P., Swe, S., et al., Genetic identification of medicinally used Salacia species by nrDNA ITS sequences and a PCR-RFLP assay for authentication of Salacia-related health foods, J. Ethnopharmacol., 2021, vol. 274, p. 113909. https://doi.org/10.1016/J.JEP.2021.113909