Abstract
Georgia plays an important role in wheat formation. In the past, the Zanduri population of Georgia was a set of diploid—Triticum monococcum var. hornemanii (2n = 14) (Gvatsa Zanduri), tetraploid Triticum timopheevii (2n = 28) (Chelta Zanduri) and hexaploid Triticum zhukovskyi Men. et Er. (2n = 42). It is a Zanduri puzzle that wild T. araraticum was not found in Georgia, though cultivated T. timopheevii was only detected here. Next-generation sequencing technologies, which have been developed in recent years, enable the determination of complete nucleotide sequences of both chloroplast and mitochondrial DNA of many higher plants, including wheat. The genetic structure of Zanduri wheat is more accurately inferred by the complete sequences of chloroplast DNA. In the present investigation, the complete sequences of three Zanduri wheats (T. timopheevii, T. zhukovskyi, and T. monococcum var. hornemanii) and wild T. araraticum are presented. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. In comparison to T. araraticum, there are 12 SNPs, a 25 bp inversion in the ccsA-ndhD intergenic sequence, and a 38-bp inversion in the intergenic sequence rbcL-rpl23 pseudogene identified in T. timopheevii and T. zhukovskyi. In addition, a 24 bp repeat of trnG-trnI intergenic sequence is present as a double copy in T. araraticum, whereas in T. timopheevii and T. zhukovskyi, it is present as a triple copy. Unlike T. araraticum, T. timopheevii and T. zhukovskyi have a 6 bp repeat in the gene ndhH, which results in a dipeptide duplication in the corresponding protein. Gvatsa Zanduri (T. monococcum var. hornemanii) chloroplast DNA slightly differs from other einkorn chloroplast DNA. In comparison to T. monococcum, four SNPs can be identified in T. monococcum (Gvatsa Zanduri), two in gene matK and one in gene ndhD. The sequenced chloroplast DNA molecules were compared to other Triticum and Aegilops species, and a phylogenetic tree was constructed. T. araraticum, T. timopheevii and T. zhukovskyi chloroplast DNA showed the closest phylogenetic relationship with the chloroplast DNA of Ae. speltoides. The most significant difference was in the 114-bp deletion within the gene ndhH in the Timopheevi species.
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References
Beridze TG, Odintsova MS, Sissakian NM (1967) Distribution of bean leaf DNA components in the cell organell fractions. Molek Biol USSR 1:142–153
Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploidy wheat under domestication. Science 316:1862–1866
Dvorak J, Luo MC, Yang ZL, Zhang HB (1998) The structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat. Theor Appl Genet 97:657–670
Gill BS, Friebe B (2002) Cytogenetics, phylogeny and evolution of cultivated wheats (2002) In: Bread wheat; FAO Plant Production and Protection Series (FAO), no. 30 Curtis, B.C., Rajaram, S., Gomez Macpherson, H. (eds.)/FAO, Rome (Italy). Plant Prod Protect Div
Guo CH, Terachi T (2005) Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops. Genes Genet Syst 80(4):277–285
Hammer K, Filatenko AA, Pistrick K (2011) Taxonomic remarks on Triticum L. and ×Triticosecale Wittm. Genet Resour Crop Evol 58:3–10
Hancock-Hanser BL, Frey A, Leslie MS, Dutton H, Archer FI, Morin PA (2013) Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics. Mol Ecolo Res 13(2):254–268
Heun M, Schaefer-Pregl R, Klawan D, Castagna R, Accerbi M, Borghi B, Salamini F (1997) Site of Einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312–1314
Kilian B, Ozkan H, Walther A, Kohl J, Dagan T, Salamini F, Martin W (2007) Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monoccum (Einkorn) domestication: implications for the origin of agriculture. Mol Biol Evol 24:2657–2668
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967
Matsuoka Y, Yamazaki Y, Ogihara Y, Tsunewaki K (2002) Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Mol Biol Evol 19(12):2084–2091
Menabde VL (1948) Wheats of Georgia. Edition of Academy of Science of Georgian SSR, Tbilisi, 272 pp. (in Russian)
Menabde VL (1961) Cultivated flora of Georgia. In: Sakhokia MF (ed) Botanical excursions over Georgia. Publishing House of the Academy of Sciences of Georgian SSR, Tbilisi, pp 69–76 (in Russian)
Menabde VL, Eritsian AA (1960) Investigation of Georgian wheat Zanduri. Soobsch Acad Sci GSSR 25:731–736
Middleton CP, Senerchia N, Stein N, Akhunov ED, Keller B, Wicker T, Kilian B (2014) Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 9:e85761
Mori N, Kondo Y, Ishii T, Kawahara T, Valkoun J, Nakamura C (2009) Genetic diversity and origin of timopheevi wheat inferred by chloroplast DNA fingerprinting. Breeding Sci 59:571–578
Ogihara Y, Terachi T, Sasakuma T (1988) Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci USA 85:8573–8577
Pagel M, Atkinson QD, Calude AS, Meade A (2013) Ultraconserved words point to deep language ancestry across Eurasia. Proc Natl Acad Sci USA 110:8471–8476
Rambaut A (2002) SE-Al Sequence alignment program. Department of Zoology, University of Oxford, UK
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16(6):276–277
Schneider A, Molnar I, Molnar-Lang M (2008) Utilisation of Aegilops (goatgrass) species to widen the genetic diversity of cultivated wheat. Euphytica 163:1–19
Tabidze V, Baramidze G, Pipia I, Gogniashvili M, Ujmajuridze L, Beridze T, Hernandez AG, Schaal B (2014) The complete chloroplast DNA sequence of eleven grape cultivars. Simultaneous resequencing methodology. Journal International des Sciences de la Vigne et du Vin J Int Sci Vigne Vin 48(2):99–109
Wang G-Z, Miyashita NT, Tsunewaki K (1997) Plasmon analysis of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs. Proc Natl Acad Sci USA 94:14570–14577
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview version 2: a multiple sequence alignment and analysis workbench. Bioinformatics 25(9):1189–1191
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255
Acknowledgments
The authors wish to acknowledge the constant interest and support of Mr. K. Bendukidze who untimely passed away on 13th November, 2014. This research was funded by the Knowledge Fund. The Knowledge Fund is a funding organization of the Free University of Tbilisi and Agricultural University of Georgia. Correction of the manuscript in terms of English was funded through the University Research Program by the U.S. Embassy in Georgia, grant No S-GE800-13-GR-122.
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P. Naskidashvili: Deceased January 15, 2015.
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Gogniashvili, M., Naskidashvili, P., Bedoshvili, D. et al. Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.). Genet Resour Crop Evol 62, 1269–1277 (2015). https://doi.org/10.1007/s10722-015-0230-x
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DOI: https://doi.org/10.1007/s10722-015-0230-x