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Development of Novel Low-Copy Nuclear Gene Primers by Transcriptomes in an Endemic Genus Orinus Hitchc. (Poaceae) from the Qinghai-Tibet Plateau

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Abstract

In the present study, a total of eleven low-copy nuclear gene markers were developed using transcriptomes for the plant genus Orinus Hitchc. (Poaceae), which comprises three species of grasses widely distributed in the Qinghai-Tibet Plateau. These developed markers were successfully amplified and sequenced for 90 individuals from nine populations of three Orinus species. The DNA sequences for the eleven loci ranged from 606 to 1152 aligned based pairs. Compared with four candidate DNA barcoding markers in our previous studies, the newly developed markers had a relatively higher number of parsimony informative sites than three cpDNA spacers (7–20 vs. 1–8), but slightly lower than those of the internal transcribed spacers (ITS). Hence, these novel low-copy nuclear gene primer pairs were validly useful for the study of phylogeography, phylogenetic analysis and population genetics. Moreover, they could be used in phylogeny reconstruction and speciation for a broad range of Orinus and even the entire subtribe Tridentinae.

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REFERENCES

  1. Qiu, Y.L., Lee, J., Bernasconi-Quadroni, F., Soltis, D.E., Solitis, P.S., Zanis, M., Zimmer, E.A., Chen, Z., Savolainen, V., and Chase, M.W., The earliest angiosperms: evidence from mitochondrial, plastid, and nuclear genomes, Nature, 1999, vol. 402, no. 6760, pp. 404–407.

    Article  CAS  PubMed  Google Scholar 

  2. Soltis, P.S., Soltis, D.E., and Chase, M.W., Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology, Nature, 1999, vol. 402, no. 6760, pp. 402–404.

    Article  CAS  PubMed  Google Scholar 

  3. Crawford, D.J., Plant macromolecular systematics in the past 50 years: one view, Taxon, 2000, vol. 49, no. 3, pp. 479–501.

    Article  Google Scholar 

  4. Rieseberg, L.H. and Soltis, D.E., Phylogenetic consequences of cytoplasmic gene flow in plants, Evol. Trends Plants, 1991, vol. 5, no. 1, pp. 65–84.

    Google Scholar 

  5. Soltis, P.S. and Soltis, D.E., Genetic variation in endemic and widespread plant species: examples from Saxifraga ceae and Polystichum (Dryopteridaceae), Aliso, 1991, vol. 13, no. 1, pp. 215–223.

    Article  Google Scholar 

  6. Sang, T., Utility of low-copy nuclear gene sequences in plant phylogenetics, Crit. Rev. Biochem. Mol. Biol., 2002, vol. 37, no. 3, pp. 121–147.

    Article  CAS  PubMed  Google Scholar 

  7. Alvarez, I. and Wendel, J.F., Ribosomal ITS sequences and plant phylogenetic inference, Mol. Phylogenet. Evol., 2003, vol. 29, no. 3, pp. 417–434.

    Article  CAS  PubMed  Google Scholar 

  8. Su, X., Wu, G.L., Li, L.L., and Liu, J.Q., Species delimitation in plants using the Qinghai-Tibetan Plateau endemic Orinus (Poaceae: Tridentinae) as an example, Ann. Bot., 2015, vol. 116, no. 1, pp. 35–48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Su, X., Liu, Y.P., Wu, G.L., Luo, W.C., and Liu, J.Q., A taxonomic revision of Orinus (Poaceae) with a new species, O. intermedius, from the Qinghai-Tibet Plateau, Novon, 2017, vol. 25, no. 2, pp. 206–213.

  10. Ghangal, R., Raghuvanshi, S., and Sharma, P.C., Isolation of good quality RNA from a medicinal plant sea buckthorn, rich in secondary metabolites, Plant Physiol. Biochem., 2009, vol. 47, nos. 11–12, pp. 1113–1115.

    Article  CAS  PubMed  Google Scholar 

  11. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q.D., Chen, Z.H., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., Palma, F.D., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., and Regev, A., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 2011, vol. 29, no. 7, pp. 644–652.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Langmead, B. and Salzberg, S., Fast gapped-read alignment with Bowtie 2, Nat. Methods, 2012, vol. 9, no. 4, pp. 357–359.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R., 1000 Genome Project Data Processing Subgroup, the sequence alignment/map format and samtools, Bioinformatics (Oxford, England), 2009, vol. 25, no. 16, pp. 2078–2079.

    Article  CAS  Google Scholar 

  14. Rozen, S. and Skaletsky, H., Primer3 on the Www for general users and for biologist programmers, Meth. Mol. Biol., 2000, vol. 132, pp. 365–386.

    CAS  Google Scholar 

  15. Pillon, Y., Johansen, J., Sakishima, T., Chamala, S., Barbazuk, W.B., Roalson, E.H., Price, D.K., and Stacy, E.A., Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations, BMC Evol. Biol., 2013, vol. 13, no. 1, p. 35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Key Laboratory of Medicinal Plant and Animal Resources in the Qinghai-Tibet Plateau, School of Life Science, Qinghai Normal University, 810008, Xining, China

    Yuping Liu, Xu Su & Ting Lv

  2. Key Laboratory of Physical Geography and Environmental Process in Qinghai Province, School of Life Science, Qinghai Normal University, 810008, Xining, China

    Yuping Liu & Ting Lv

  3. Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Life Science, Qinghai Normal University, 810008, Xining, China

    Xu Su & Kelong Chen

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  1. Yuping Liu
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  2. Xu Su
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  3. Ting Lv
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  4. Kelong Chen
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Correspondence to Xu Su.

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Yuping Liu, Su, X., Lv, T. et al. Development of Novel Low-Copy Nuclear Gene Primers by Transcriptomes in an Endemic Genus Orinus Hitchc. (Poaceae) from the Qinghai-Tibet Plateau. Cytol. Genet. 53, 261–265 (2019). https://doi.org/10.3103/S0095452719030113

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