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Development of novel lowcopy nuclear gene primers by transcriptomes in an endemic genus Orinus Hitchc. (Poaceae) from the QinghaiTibet Plateau
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 variable 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.
Key words: Poaceae; Orinus; transcriptome; low-copy nuclear gene; primer; next-generation sequencing
E-mail: xusu8527972 126.com
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.
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.
3. Crawford, D.J., Plant macromolecular systematics in the past 50 years: one view, Taxon, 2000, vol. 49, no. 3, pp. 479–501.
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.
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.
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.
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.
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.
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.
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.
12. Langmead, B. and Salzberg, S., Fast gapped-read alignment with Bowtie 2, Nat. Methods, 2012, vol. 9, no. 4, pp. 357–359.
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.
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.
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.
|Coded & Designed by Volodymyr Duplij||Modified 10.04.21|