Altı DNA bölgesinin bazı Polygalaceae’de Maximum Likelihood (ML) ve TaxonDNA yöntemleri ile in slico olarak değerlendirilmesi

Polygalaceae kozmopolit bir yayılıma sahip, 27 cins içinde yaklaşık 1,200 türe sahip geniş bir familyadır. Ancak birçok bitki grubu gibi, Polygalaceae türlerinin tanımlanması genellikle çiçek ve meyva karakterlerine bağlıdır. Bu nedenle DNA barkodlama yontemi steril materyalin doğru tanımlanmasını sağlayabilir. Bu çalışmada altı tane yaygın olarak kullanılan DNA barkodu, rbçL, matK, trnL-F DNA bölgesi (trnL intron+trnL-F dahil), tüm ITS (ITS1+5.8S+ITS2), ITS1 ve ITS2 DNA bölgelerinin, Maximum Likelihood (ML) ve TaxonDNA yöntemleri ile DNA barkodu olarak performansları değerlendirilmiştir. Sonuçlar göstermiştir ki, altı DNA bölgesinden hiçbiri ideal değildir, ancak Polygalaceae familyası için en uygun DNA barkodu matK gen bölgesidir.

An in-silico approach for the evaluation of six DNA barcodes by using Maximum Likelihood (ML) and TaxonDNA approaches for some Polygalaceae

Polygalaceae is a large family with a cosmopolitan distribution, comprising ca. 1,200 species in 27 genera. However, similar to many plant groups, the identification of Polygalaceae species mostly depends on floral and fruit characteristics; therefore, DNA barcoding could easily warrant the correct identification of sterile material. In the current study, the utility of six widely employed plant DNA barcode loci, namely rbcL, matK, trnL-F region (including trnL intron+trnL-F intergenic spacer), the entire ITS (ITS1+5.8S+ITS2) as well as subunits ITS1 and ITS2 have been explored by performing Maximum Likelihood (ML) and TaxonDNA analyses. The results have shown that, while none of the six loci reviewed here completely fulfils the ideal DNA barcoding criteria; yet, matK region is the most useful DNA barcode for the Polygalaceae.

PDF

___

Alvarez, I., and Wendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29(3):417– 434. doi:10.1016/S1055-7903(03)00208-2.
Aygoren Uluer, D. and Alshamrani, R., 2019. DNA barcoding of a complex genus, Aesculus L. (Sapindaceae) reveals lack of species-level resolution. Botany, 97(9), 503-512.
Baldwin, B.G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Molecular Phylogenetics and Evolution, 1(1): 3–16. doi:10.1016/1055-7903(92)90030-K.
CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106(31): 12794– 12797. doi: 10.1073/pnas.0905845106.
Chase, M.W., Cowan, R.S., Hollingsworth, P.M., van den Berg, C., Madrinan, S., Petersen, G. et al. 2007. A proposal for a standardised protocol to barcode all land plants. Taxon, 56(2): 295–299. doi:10.1002/tax.562004.
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L. et al. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One, 5(1): e8613. doi:10.1371/journal.pone.0008613.
Clement, W.L., and Donoghue, M.J. 2012. Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms. BMC Evolutionary Biology, 12(1): 73. doi:10.1186/1471-2148-12-73.
Cowan, R.S., Chase, M.W., Kress, W.J., and Savolainen, V. 2006. 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon, 55(3): 611–616. doi:10.2307/25065638.
Forest, F., Chase, M.W., Persson, C., Crane, P.R. and Hawkins, J.A., 2007. The role of biotic and abiotic factors in evolution of ant dispersal in the milkwort family (Polygalaceae). Evolution, 61(7), 1675-1694.
Hajibabaei, M., Singer, G.A., Hebert, P.D., and Hickey, D.A. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23(4): 167–172. doi:10.1016/j.tig.2007.02.001.
Han, J., Liu, C., Li, M., Shi, L., Song, J., Yao, H., Pang, X. and Chen, S., 2010. Relationship between DNA barcoding and chemical classification of Salvia medicinal herbs. Chinese Herbal Medicines, 2(1), 16-29.
Han, J., Zhu, Y., Chen, X., Liao, B., Yao, H., Song, J., Chen, S. and Meng, F., 2013. The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS. BioMed Research international, 2013.
Hebert, P.D., and Ratnasingham, S., and deWaard, J.R. 2003a. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences, 270 (Suppl 1): S96– S99. doi:10.1098/rsbl.2003.0025.
Hebert, P.D., Cywinska, A., and Ball, S.L., and deWaard, J.R. 2003b. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512): 313–321. doi:10.1098/rspb. 2002.2218.
Hebert, P.D., Penton, E.H., Burns, J.M., Janzen, D.H., and Hallwachs, W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101(41): 14812–14817. doi:10.1073/pnas.0406166101.
Hollingsworth, P.M., Graham, S.W. and Little, D.P., 2011. Choosing and using a plant DNA barcode. PloS One, 6(5), p.e19254.
Kartzinel, T.R., Chen, P.A., Coverdale, T.C., Erickson, D.L., Kress, W.J., Kuzmina, M.L., Rubenstein, D.I., Wang, W. and Pringle, R.M., 2015. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proceedings of the National Academy of Sciences of the United States of America, 112(26), 8019-8024.
Kearse, M., Moir, R., Wilson, A., StonesHavas, 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(12): 1647– 1649. doi:10.1093/bioinformatics/bts199.
Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A., and Janzen, D.H. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America, 102(23): 8369–8374. doi: 10.1073/pnas.0503123102.
Kress, W.J. and Erickson, D.L., 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PloS One, 2(6), p.e508.
Kuzmina, M.L., Johnson, K.L., Barron, H.R. and Hebert, P.D., 2012. Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library. BMC Ecology, 12(1), 1-11.
Lahaye, R., Van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G. and Savolainen, V., 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 2923-2928.
Liu, J., Milne, R.I., Möller, M., Zhu, G.F., Ye, L.J., Luo, Y.H., Yang, J.B., Wambulwa, M.C., Wang, C.N., Li, D.Z. and Gao, L.M., 2018. Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification. Molecular Ecology Resources, 18(5), 1115-1131.
Marghali, S., Fadhlaoui, I., Gharbi, M., Zitouna, N. and Trifi-Farah, N., 2015. Utility of ITS2 sequence data of nuclear ribosomal DNA: Molecular evolution and phylogenetic reconstruction of Lathyrus spp. Scientia Horticulturae, 194, 313-319.
Meier, R., Shiyang, K., Vaidya, G. and Ng, P.K., 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology, 55(5), 715-728.
Newmaster, S.G., Fazekas, A.J., and Ragupathy, S. 2006. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Botany, 84(3): 335–341. doi:10.1139/b06-047.
Newmaster, S.G., Fazekas, A.J., Steeves, R.A.D., and Janovec, J. 2008. Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Resources, 8(3): 480–490. doi:10.1111/j.1471-8286.2007.02002.x.
Parveen, I., Gafner, S., Techen, N., Murch, S.J. and Khan, I.A., 2016. DNA barcoding for the identification of botanicals in herbal medicine and dietary supplements: strengths and limitations. Planta Medica, 82(14), 1225-1235.
Pastore, J.F.B., Abbott, J.R., Neubig, K.M., Whitten, W.M., Mascarenhas, R.B., Mota, M.C.A. and van den Berg, C., 2017. A molecular phylogeny and taxonomic notes in Caamembeca (Polygalaceae). Systematic Biology, 42(1), 54-62.
Shi, L.C., Zhang, J., Han, J.P., Song, J.Y., Yao, H., Zhu, Y.J., LI, J.C., Wang, Z.Z., Xiao, W., Lin, Y.L. and Xie, C.X., 2011. Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae. Journal of Systematics and Evolution, 49(3), 261-266.
Schlötterer, C., Hauser, M.T., von Haeseler, A. and Tautz, D., 1994. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Molecular Biology and Evolution, 11(3), 513-522.
Stamatakis, A., Hoover, P., and Rougemont, J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57(5): 758–771. doi:10.1080/10635150802429642.
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C. and Willerslev, E., 2007. Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35(3), e14-e14.
Xin, T., Yao, H., Gao, H., Zhou, X., Ma, X., Xu, C., Chen, J., Han, J., Pang, X., Xu, R. and Song, J., 2013. Super food Lycium barbarum (Solanaceae) traceability via an internal transcribed spacer 2 barcode. Food Research International, 54(2), 1699-1704.
Yao, H., Song, J., Liu, C., Luo, K., Han, J., Li, Y. et al. 2010. Use of ITS2 region as the universal DNA barcode for plants and animals. PloS One, 5(10): e13102. doi:10.1371/journal.pone.0013102.
Zhu, S., Li, Q., Chen, S., Wang, Y., Zhou, L., Zeng, C. and Dong, J., 2018. Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure. Pharmaceutical Biology, 56(1), 548-558.