Advertisement

Genetic Resources and Crop Evolution

, Volume 62, Issue 8, pp 1269–1277 | Cite as

Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.)

  • M. Gogniashvili
  • P. Naskidashvili
  • D. Bedoshvili
  • A. Kotorashvili
  • N. Kotaria
  • T. Beridze
Research Article

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.

Keywords

Chloroplast DNA Illumina Indels Phylogeny Sequencing SNP Triticum spp. Wheat 

Notes

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.

References

  1. Beridze TG, Odintsova MS, Sissakian NM (1967) Distribution of bean leaf DNA components in the cell organell fractions. Molek Biol USSR 1:142–153Google Scholar
  2. Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploidy wheat under domestication. Science 316:1862–1866CrossRefPubMedGoogle Scholar
  3. 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 97:657–670CrossRefGoogle Scholar
  4. 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 DivGoogle Scholar
  5. Guo CH, Terachi T (2005) Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops. Genes Genet Syst 80(4):277–285CrossRefPubMedGoogle Scholar
  6. Hammer K, Filatenko AA, Pistrick K (2011) Taxonomic remarks on Triticum L. and ×Triticosecale Wittm. Genet Resour Crop Evol 58:3–10CrossRefGoogle Scholar
  7. 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):254–268CrossRefGoogle Scholar
  8. 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 278:1312–1314CrossRefGoogle Scholar
  9. 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 24:2657–2668CrossRefPubMedGoogle Scholar
  10. 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 25:1966–1967CrossRefPubMedGoogle Scholar
  11. 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):2084–2091CrossRefPubMedGoogle Scholar
  12. Menabde VL (1948) Wheats of Georgia. Edition of Academy of Science of Georgian SSR, Tbilisi, 272 pp. (in Russian)Google Scholar
  13. 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)Google Scholar
  14. Menabde VL, Eritsian AA (1960) Investigation of Georgian wheat Zanduri. Soobsch Acad Sci GSSR 25:731–736Google Scholar
  15. 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:e85761PubMedCentralCrossRefPubMedGoogle Scholar
  16. 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 59:571–578CrossRefGoogle Scholar
  17. 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 85:8573–8577PubMedCentralCrossRefPubMedGoogle Scholar
  18. Pagel M, Atkinson QD, Calude AS, Meade A (2013) Ultraconserved words point to deep language ancestry across Eurasia. Proc Natl Acad Sci USA 110:8471–8476PubMedCentralCrossRefPubMedGoogle Scholar
  19. Rambaut A (2002) SE-Al Sequence alignment program. Department of Zoology, University of Oxford, UKGoogle Scholar
  20. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16(6):276–277CrossRefPubMedGoogle Scholar
  21. Schneider A, Molnar I, Molnar-Lang M (2008) Utilisation of Aegilops (goatgrass) species to widen the genetic diversity of cultivated wheat. Euphytica 163:1–19CrossRefGoogle Scholar
  22. 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):99–109Google Scholar
  23. 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 94:14570–14577PubMedCentralCrossRefPubMedGoogle Scholar
  24. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview version 2: a multiple sequence alignment and analysis workbench. Bioinformatics 25(9):1189–1191PubMedCentralCrossRefPubMedGoogle Scholar
  25. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • M. Gogniashvili
    • 1
  • P. Naskidashvili
    • 3
  • D. Bedoshvili
    • 3
  • A. Kotorashvili
    • 2
  • N. Kotaria
    • 2
  • T. Beridze
    • 1
  1. 1.Institute of Molecular GeneticsAgricultural University of GeorgiaTbilisiGeorgia
  2. 2.National Centre for Disease Control and Public HealthTbilisiGeorgia
  3. 3.Agricultural University of GeorgiaTbilisiGeorgia

Personalised recommendations