Phylogeny of Korean Opuntia spp. based on multiple DNA regions

Although Opuntia species are of high agronomic value in Korea, the taxonomic position of Korean Opuntia species has never been investigated. The taxonomic position of Korean Opuntia spp. Within the tribe Opuntieae was examined based on DNA sequence analysis of matK, trnL-F, atpB-rbcl, and ITS regions. The total amplified sequence length was 2977 bp; only 18 parsimonious informative sites were present, even though they belonged to different species. A phylogenetic tree using both the maximum likelihood method with 2000 bootstrap replications and Bayesian posterior probabilities was constructed. The new forma, Opuntia humifusa f. Jeollaensis, used in this study was placed within the Macrocentra clade rather than the Humifusa clade. The genetic distance between O. Humifusa f. Jeollaenis and O. Camanchica was the lowest among all Opuntia spp. Analyzed in this study. Korean O. Ficus-indica was genetically closer to O. Engelmannii than to O. Ficus-indica previously reported. Opuntia engelmannii and O. Ficus-indica have been considered conspecific previously, and so it is likely that the Korean O. Ficus-indica used in this study may be a relative of O. Engelmannii or may have arisen from a lineage different to the O. Ficus-indica used in the analysis.

Anahtar Kelimeler:

Korean Opuntia, phylogeny, matK, trnL-F, atpB-rbcL, ITS region

Phylogeny of Korean Opuntia spp. based on multiple DNA regions

Keywords:

Korean Opuntia, phylogeny, matK, trnL-F, atpB-rbcL, ITS region,

PDF

___

Ahn DK (1988). Illustrated Book of Korean Medicinal Herbs. Seoul, Korea: Kyohaksa Ltd. Anderson EF (2001). The Cactus Family. Portland, OR, USA: Timber Press.
Baldwin BG (1992). Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Mol Phylogenet Evol 1: 3–16.
Barthlott W, Hunt DR (1993). Cactaceae. In: Kubitzki K, Rohwer JG, Bittrich V, editors. The Families and Genera of Vascular Plants, vol. 2. Berlin, Germany: Springer Verlag, pp. 161–197.
Benson L (1982). The Cacti of the United States and Canada. Stanford, CA, USA: Stanford University Press.
Benson L, Walkington DL (1965). The southern Californian prickly pears: invasion, adulteration, and trial-by-fire. Ann Mol Bot Gard 52: 252–273.
Britton NL, Rose JN (1919). The Cactaceae. Washington DC, USA: Carnegie Institute of Washington.
Doyle JJ, Doyle JL (1990). Isolation of plant DNA from fresh tissue. Focus 12: 13–15.
Engelmann G (1856). Synopsis of the Cactaceae of the territory of the United States and adjacent regions. P Natl Acad Sci USA 3: 259–346.
De Salle R, Brower AVZ (1997). Process partitions, congruence and independence of characters: inferring relationships among closely related Hawaiian Drosophila from multiple gene regions. Syst Bot 46: 751–764.
De Lyra MCC, Santos DC, Mondragon-Jacobo C, Da Silva MLRB, Mergulhao ACES, Martinez-Romero E (2013). Molecular characteristics of prickly-pear cactus (Opuntia) based on internal transcribed spacer sequences (ITS) of Queretaro State – Mexico. J App Bio Biotech 1: 6–10.
Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
Go HD, Lee KH, Kim HJ, Lee EH, Lee J, Song YS, Lee YH, Jin C, Lee YS, Cho J (2003). Neuroprotective effects of antioxidative flavonoids, quercetin, (+)-dihydroxyquercetin and quercetin 3-methyl ether, isolated from Opuntia ficus indica var. saboten. Brain Res 965: 130–136.
Griffith MP (2003). Using molecular data to elucidate reticulate evolution in Opuntia. Madrono 50: 162–169.
Griffith MP (2004). The origins of an important cactus crop, Opuntia ficus-indica (Cactaceae): new molecular evidence. Am J Bot 91: 1915–1921.
Griffith MP, Porter JM (2009). Phylogeny of Opuntioideae (Cactaceae). Intl J Plant Sci 170: 107–116.
Hall TA (1999). Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symposium Series 41: 95–98.
Hernandez TH, Hernandez HM, Arturo De-Nova J, Puente R, Eguiarte LE, Magallon S (2011). Phylogenetic relationships and evolution of growth form in Cactaceae (Caryophyllales, Eudicotyledoneae). Am J Bot 98: 44–61.
Hillis DM, Bull JJ (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analyses. Syst Biol 42: 182–192.
Huang X, Li Q, Zhang Y, Lu Q, Guo L, Huang L, He Z (2008). Neuroprotective effects of cactus polysaccharide on oxygen and glucose deprivation induced damage in rat brain slices. Cell Mol Neurobiol 28: 559–568.
Hunt DR (2006). The New Cactus Lexicon. 1st ed. Milborne Port, UK: DH Books.
Inglese P, Basile F, Schirra M (2002). Cactus pear fruit production. In: Nobel PS, editor. Cacti: Biology and Uses. Berkeley, CA, USA: University of California Press, pp. 163–183.
Kim H, Park S (2009). Metabolic profiling and discrimination of two cacti cultivated in Korea using HPLC-ESI-MS and multivariate statistical analysis. J Korean Soc Appl Biol Chem 52: 346–352.
Kim EJ, Srikanth K, Lee E, Whang SS (2014). Opuntia humifusa (Raf.) Raf.f. jeollaensis E.J.Kim & S.S. Whang, a new forma based on three DNA markers. Korean Journal of Plant Taxonomy 44: 181–187.
Laurenz JC, Collier CC, Kuti JO (2003). Hypoglycaemic effect of Opuntia lindheimeri Engelm. in a diabetic pig model. Phytother Res 17: 26–29.
Lee J, Koo N, Min DB (2004). Reactive oxygen species, aging, and antioxidant nutraceuticals. Compr Rev Food Sci 3: 21–33.
Majure LC, Judd WS, Soltis PS, Soltis DE (2012a). Cytogeography of the Humifusa clade of Opuntia s.s. Mill. 1754 (Cactaceae: Opuntioieae): correlations with geographic distributions and morphological differentiation of a polyploid complex. Comp Cytogenet 6: 53–77.
Majure LC, Puente R, Griffith MP, Judd WS, Soltis PM, Soltis DE (2012b). Phylogeny of Opuntia s.s. (Cactaceae): clade delineation, geographic origins and reticulate evolution. Am J Bot 99: 847–864.
Ncibi S, Othman MB, Akacha A, Krifi MN, Zourgui L (2008). Opuntia ficus indica extract protects against chlorpyrifosinduced damage on mice liver. Food Chem Toxicol 46: 797– 802.
Nei M, Kumar S (2000). Molecular Evolution and Phylogenetics. New York, NY, USA: Oxford University Press.
Nyeffler R, Eggli U (2010). A farewell to dated ideas and concepts: molecular phyogenetics and a revised suprageneric classification of the family Cactaceae. Schumannia 6: 109–149.
Ostolaza C (1994). Cactus y etnobotanica. Quepo 8: 79–86 (article in Spanish).
Parfitt BD, Pinakava DJ (1988). Nomenclatural and systematic reassessment of Opuntia engelmannii and O. lindheimeri (Cactaceae). Modrono 35: 342–349.
Park EH, Chun MJ (2001). Wound healing activity of Opuntia ficusindica. Fitoterapia 72: 165–167.
Pinkava DJ (2003). Vascular plants of Arizona: Cactaceae. Part Six. Opuntia P. Miller. J Arizona Nevada Acad Sci 35: 137–150.
Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253–1256.
Ronquist F, Huelsenbeck JP (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
Stintzing FC, Herbach KM, Mosshammer MR, Carle R, Yi W, Sellappan S, Akoh CC, Bunch R, Felker P (2005). Color, betalain pattern, and antioxidant properties of cactus pear (Opuntia spp.) clones. J Agric Food Chem 53: 442–451.
Stuppy W (2001). A new combination in Tephrocactus Lem. (Cactaceae). Kew Bull 56: 1003–1005.
Sorenson MD, Franzosa EA (2007). TreeRot, version 3. Boston: Boston University.
Tamura K (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol 9: 678–687.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876–4882.
Trejo Gonzalez A, Gabriel Ortiz G, Puebla Perez M, Huizar Contreras MD, Munguia Mazariegos MR, Mejia Arreguin S, Calva E (1996). Extract from prickly pear cactus (Opuntia fuliginosa) controls experimentally induced diabetes in rats. J Ethnopharmacol 55: 27–33.
Wallace RS, Gibson AC (2002). Evolution and Systematics. In: Nobel PS, editor. Cacti: Biology and Uses. Berkeley, CA, USA: University of California Press, pp. 1–21.
White TJ, Bruns T, Lee S, Taylor J (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR Protocols: a Guide to Methods and Applications. San Diego, CA, USA: Academic Press, pp. 315–322.