Evidence map›Paper›PMID 28785866›Full record

ArticleMolecular genetics and genomics : MGG2017

Whole genome comparative analysis of four Georgian grape cultivars.

V Tabidze, I Pipia, M Gogniashvili, N Kunelauri, L Ujmajuridze, M Pirtskhalava, B Vishnepolsky, A G Hernandez, C J Fields, Tengiz Beridze

Abstract readComparative StudyValidation Study
PubMed Publisher
In one paragraph

Article in Molecular genetics and genomics : MGG, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
3.0field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 2 countries.

V TabidzeInstitute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia.
I PipiaInstitute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia.
M GogniashviliInstitute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia.
N KunelauriInstitute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia.
L UjmajuridzeAgricultural Scientific-Research Center, 6 Marshal Gelovani Ave, 0159, Tbilisi, Georgia.
M PirtskhalavaIvane Beritashvili Center of Experimental Biomedicine, Gotua St. 14, 0160, Tbilisi, Georgia.
B VishnepolskyIvane Beritashvili Center of Experimental Biomedicine, Gotua St. 14, 0160, Tbilisi, Georgia.
A G HernandezRoy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
C J FieldsHigh 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.
Tengiz BeridzeInstitute of Molecular Genetics, Agricultural University of Georgia, # 240 David Aghmashenebeli Alley, 0159, Tbilisi, Georgia. t.beridze@agruni.edu.ge.
Agricultural University of Georgia · GEUniversity of Illinois Urbana-Champaign · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Genome, PlantAlkyl and Aryl TransferasesChromosomes, PlantDNA, MitochondrialDNA, PlantPolymorphism, Single NucleotideVitisAlkyl and Aryl TransferasesDNA, MitochondrialDNA, Plantterpene synthaseGrapeIlluminaMitochondrial DNANuclear DNASequencingSNP

Identifiers

PMID28785866
OpenAlexW2743336883

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.