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Whole genome comparative analysis of four Georgian grape cultivars

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Abstract

Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars—Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference. Mitochondrial DNA of Chkhaveri closely matches that of the reference Pinot noir mitochondrial DNA, with the exception of 16 SNPs found in the Chkhaveri mitochondrial DNA. The number of SNPs in mitochondrial DNA from Saperavi, Meskhetian green, and Rkatsiteli was 764, 702, and 822, respectively. Nuclear DNA differs from the reference by 1,800,675 nt in Chkhaveri, 1,063,063 nt in Meskhetian green, 2,174,995 in Saperavi, and 5,011,513 in Rkatsiteli. Unlike mtDNA Pinot noir, chromosomal DNA is closer to the Meskhetian green than to other cultivars. Substantial differences in the number of SNPs in mitochondrial and nuclear DNA of Chkhaveri and Pinot noir cultivars are explained by backcrossing or introgression of their wild predecessors before or during the process of domestication. Annotation of chromosomal DNA of Georgian grape cultivars by MEGANTE, a web-based annotation system, shows 66,745 predicted genes (Chkhaveri—17,409; Saperavi—17,021; Meskhetian green—18,355; and Rkatsiteli—13,960). Among them, 106 predicted genes and 43 pseudogenes of terpene synthase genes were found in chromosomes 12, 18 random (18R), and 19. Four novel TPS genes not present in reference Pinot noir DNA were detected. Two of them—germacrene A synthase (Chromosome 18R) and (−) germacrene D synthase (Chromosome 19) can be identified as putatively full-length proteins. This work performs the first attempt of the comparative whole genome analysis of different haplogroups of Vitis vinifera cultivars. Based on complete nuclear and mitochondrial DNA sequence analysis, hypothetical phylogeny scheme of formation of grape cultivars is presented.

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Acknowledgements

This research was funded by Mr. Kakha Bendukidze via his Knowledge Fund, a funding organization of the Free University of Tbilisi and Agricultural University of Georgia. Mr. K. Bendukidze untimely passed away on 13 November 2014.

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Authors and Affiliations

  1. Institute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia

    V. Tabidze, I. Pipia, M. Gogniashvili, N. Kunelauri & Tengiz Beridze

  2. Agricultural Scientific-Research Center, 6 Marshal Gelovani Ave, 0159, Tbilisi, Georgia

    L. Ujmajuridze

  3. Ivane Beritashvili Center of Experimental Biomedicine, Gotua St. 14, 0160, Tbilisi, Georgia

    M. Pirtskhalava & B. Vishnepolsky

  4. Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    A. G. Hernandez

  5. High Performance Computing in Biology, Roy J. Carver Biotechnology Center, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    C. J. Fields

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  1. V. Tabidze
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  2. I. Pipia
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  10. Tengiz Beridze
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Correspondence to Tengiz Beridze.

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Tabidze, V., Pipia, I., Gogniashvili, M. et al. Whole genome comparative analysis of four Georgian grape cultivars. Mol Genet Genomics 292, 1377–1389 (2017). https://doi.org/10.1007/s00438-017-1353-x

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