The first molecular identification of Egyptian Miocene petrified dicot woods (Egyptians’ dream becomes a reality)
DOI:
https://doi.org/10.13128/caryologia-750Keywords:
Egyptian petrified woods, aDNA, DNA barcoding, ITSAbstract
This is the first work on Egyptian ancient DNA (aDNA) from plant fossil remains. Two aDNA extracts from Miocene petrified dicot woods were successfully obtained, amplified, sequenced and recorded for the first time in the world using a DNA barcoding technique. Internal transcribed spacers (ITS) barcoding is a technique for delimiting and identifying specimens using standardized DNA regions. The two Miocene dicot woods: Bombacoxylon owenii (Malvaceae/Bombacoideae) and
Dalbergioxylon dicorynioides (Leguminosae/Papilionoideae) were collected from the Wadi Natrun area in Egypt and were identified by palaeobotanists on the basis of wood anatomy. The molecular identification by ITS region of Bombacoxylon owenii did not match the wood taxonomic assignation. The molecular identification of
Bombacoxylon owenii suggested that it is more related to the extant genus Ceiba rather than to the extant genus Bombax. In contrast, the molecular identification by ITS of Dalbergioxylon dicorynioides matched the identification of the palaeobotanist (related to extant genus Dalbergia). Therefore, we suggest that this region should be used as a starting point to identify several plant fossil remains and this work will be helpful in solving problems related to the identification of plant fossils.
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References
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Thompson JD, Higgins DG, Gibson TG. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Aci Res. 22: 4673-4680.
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White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNAgenes for phylogenetics. In: Innis MA, Gelfard H, Sninsky JS, WhiteTJ (eds) PCR-protocols and applications. A laboratory manual. New York: Academic Press, pp 315–322.
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Wood data base available at inside wood home page. 2013. Online search of fossil and modern.
Yao H, Song J, Liu C, Luo K, Han J, Li Y, et al. 2010. Use of IRS2 region as the universal DNA barcode for plants and animals. PLoS ONE 5: e13102. doi.org/10.1371/journal.pone.0013102
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: e8613. doi.org/10.1371/journal.pone.0008613
Deguilloux MF, Bertel L, Celant A, Pemonge MH, Sadori L, Magri D, Petit RJ. 2006. Genetic analysis of archaeological wood remains: first results and prospects, J Archaeol Sci. 33: 1216–1227.
Deguilloux MF, Petit MH, Pemonge RJ. 2002. Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proc R Soc London. 269: 1039-1046.
Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytoch Bull. 19: 11-15.
El-Saadawi W, Kamal El-Din MM, Darwish MH, Osman R. 2014. African Miocene dicot woods with two new records for this epoch from Egypt. Taeckholmia. 34:1-2.
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evol. 39: 783-791.
Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I. 2005. Assessing ancient DNA studies. Tren Ecol Evol. 20: 541–544.
Golberg EM, Brown TA, Bada JL, Westbroek P, Bishop MJ, Dover GA. 1991. Amplification and analysis of Miocene plant fossil DNA. Phil Trans R Soc Lond B. 333: 419-427.
Golenberg EM. 1994. Fossil samples DNA from plant compression fossils. In: Herrmann B, Hummel S, (eds) Ancient DNA recovery and analysis of genetic material from paleontological, archaeological, museum, medical, and forensic specimens. New York: Springer-Verlag Inc pp 237-256.
Goloubinoff P, Pääbo S, Wilson A. 1993. Evolution of Maize Inferred from Sequence Diversity of an adh2 Gene Segment from Archaeological Specimens. Proc Natl Acad Sci USA. 90:1997-2001.
Gugerli F, Parducci L, Petit RJ. 2005. Ancient plant DNA: review and prospects, New Phytologist. 166: 409–418.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3): 307–321.
Gyulai G, Humphreys M, Lagler R, Szabó Z, Tóth Z, Bittsánszky A, Gyulai F, Heszky L. 2006. Seed remains of common millet from the 4th (Mongolia) and 15th (Hungary) Centuries: AFLP, SSR and mtDNA sequence recoveries. Seed Sci Res. 16: 179-191.
Han J, Zhu Y, Chen X, Liao B, Yao H, Song J, Chen S, et al. 2013. The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS. Biomed Res Int. 2013:741476. doi.org/10.1155/2013/741476
Hamalton T. 2016. DNA from ancient wood. Van Sangyan. 3: 27-30.
Helentjaris T. 1988. Maize Genet Coop. News Lett. 62: 104-105.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and using a plant DNA barcode. PLoS ONE. 6: e19254. doi.org/10.1371/journal.pone.0019254
Kaestle AF, Horsburgh KA. 2002. Ancient DNA in anthropology: methods, applications, and ethics. Am J Phys Anthropol. 35: 92-130.
Kamal EL-Din MM, Darwish MH, EL-Saadawi W. 2015. Novelties on Miocene woods from Egypt with a summary on African fossil woods of Fabaceae, Malvaceae and Dipterocarpaceae. Palaeontographica Abt B. 292:173-199.
Kim S, Soltis DE, Soltis PS, Suh Y. 2004. DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcl sequence of Persea pseudocarolinensis (Lauraceae). Am J Bot . 91: 615–620.
Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16: 111-120.
Liepelt S, Sperisen C, Deguilloux MF, Petit RJ, Kissling R, Spencer M, De Beaulieu J, Taberlet P, Gielly l, Ziegenhagen B. 2006. Authenticated DNA from Ancient Wood Remains. Ann Bot. 98: 1107–1111.
Li YW, Zhou X, Feng G, Hu HY, Niu LM, Hebert PD, et al. 2010. COI and ITS2 sequences delimit species, reveal cryptic taxa and host specificity of fig-associated Sycophila (Hymenoptera, Eurytomidae). Mol Ecol Resour 10: 31–40.
Marota I, Basile C, Ubaldi M, Rollo F. 2002. DNA decay rate in Papyri and human remains from Egyptian archaeological sites. Am j phys anthropol. 117:310–318.
Nasab HM, Mardi M, Talaee H, Nashli HF, Pirseyedi SM, Nobari AH, Mowla SJ. 2010. Molecular analysis of ancient DNA extracted from 3250-3450 year-old plant seeds excavated from Tepe Sagz Abad in Iran. J Agr Sci Tech. 12: 459-470.
Nordahlia AS, Noraini T, Chung RCK, Lim SC, Nadiah I, Azahana NA, Solihani NS. 2016. Comparative wood anatomy of three Bombax species and Ceiba pentandra (Malvaceae: Bombacoideae) in Malaysia. Mal Nat J. 68: 203-216.
Poinar HN, Cano RJ, Poinar GO. 1993. DNA from an extinct plant. Nature 363: 677.
Rogers SO, Bendich AJ. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummi- fied plant tissues. Pl molec Biol. 5: 69-76.
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30: 2725-2729.
Thompson JD, Higgins DG, Gibson TG. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Aci Res. 22: 4673-4680.
Tripathi AM, Tyagi A, Kumar A, Singh A, Singh S, Chaudhary LB, Roy S. 2013. The internal transcribed spacer (ITS) region and trnhHpsbA are suitable candidate loci for DNA barcoding of tropical tree species of India. PloS ONE. 8: e57934. doi.org/10.1371/journal.pone.0057934.
van Nues R W, Rientjes J M J, van der Sande C A F M., Zerp S F, Sluiter C, Venema J, Planta R J, Raue´ HA. 1994. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucl Aci Res. 22: 912–919.
Wagner S, Lagane F, Seguin-Orlando A, et al. 2018 High-Throughput DNA sequencing of ancient wood. Mol Ecol. 27: 1138-1154.
White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNAgenes for phylogenetics. In: Innis MA, Gelfard H, Sninsky JS, WhiteTJ (eds) PCR-protocols and applications. A laboratory manual. New York: Academic Press, pp 315–322.
Wickens GE. 2008. The Baobabs: Pachycauls of Africa, Madagascar and Australia Springer Science & Business Media
Wood data base available at inside wood home page. 2013. Online search of fossil and modern.
Yao H, Song J, Liu C, Luo K, Han J, Li Y, et al. 2010. Use of IRS2 region as the universal DNA barcode for plants and animals. PLoS ONE 5: e13102. doi.org/10.1371/journal.pone.0013102
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Published
2020-03-13
How to Cite
Sobieh, S. S., & Darwish, M. H. (2020). The first molecular identification of Egyptian Miocene petrified dicot woods (Egyptians’ dream becomes a reality). Caryologia, 73(2), 3–13. https://doi.org/10.13128/caryologia-750
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