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Tevdoradze E.,George Eliava Institute for Bacteriophages | Farlow J.,Pennsylvania State University | Farlow J.,Farlow Scientific Consulting Company | Kotorashvili A.,Lugar Center for Public Health Research | And 6 more authors.
Virology Journal

Background: Recently the genome sequences of two brucellaphages, isolated in Georgia (Tb) and Mexico (Pr) were reported revealing pronounced sequence homogeneity and the presence of two major indels discriminating the two phages. Subsequent genome sequencing of six diagnostic brucellaphages: Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C phages identified three major genetic groups. However, the propensity for fine-scale genetic variability of diverse brucellaphages grown on multiple hosts within a single Brucella species remains unknown. Methods: We sequenced the complete genomes of ten brucellaphages following initial propagation on B. abortus strain 141 and after subsequent propagation on B. abortus strain S19. All brucellaphages were isolated and propagated at the Eliava Institute including the original Tb phage. Genomic libraries were quantified using the Qbit and sheared on the Covaris M220. QC for fragmentation was performed on the BioAnalyzer 2100. DNA libraries were prepared using an Illumina Paired-End protocol and sequenced on the Illumina MiSeq. Sequence analysis was performed using Geneious and MEGA software. Results: Comparative whole genome sequence analysis revealed genetic homogeneity consistent with previously published data as well as multiple nucleotide variations. Genomic changes as a result of passages were observed in similar genes and predominantly occurred at identical sites in separate phages. Multiple instances of within-sample genetic heterogeneity were observed often at shared genomics positions across phages. Positive selection was detected in the tail collar protein gene. We also identified a Staphylothermus marinus F1-like CRISPR spacer and sequences orthologous to both prophage antirepressors of Brucella spp. and intergenic sequences encoded by Ochrobactrum anthropi. Conclusion: We surveyed whole genome level diversity in phage lytic for B. abortus as they are propagated on alternate vaccine strains within the species. Our data extend previous results indicating select variable hotspots and broad genomic homogeneity as well as multiple common polymorphisms and within-sample variation. These data also provide additional genomes for future reference in comparative studies involving the molecular evolution and host specificity of brucellaphages. © 2015 Tevdoradze et al.; licensee BioMed Central. Source

Pipia I.,Agricultural University of Georgia | Gogniashvili M.,Agricultural University of Georgia | Tabidze V.,Agricultural University of Georgia | Kotorashvili A.,Lugar Center for Public Health Research | Kotaria N.,Lugar Center for Public Health Research
Acta Horticulturae

Caucasus region is widely believed to be the area in which grape domestication began, and the study of genetic diversity of wild grape samples in this region is viewed as a key to understanding grape domestication in general. The primary goal of this research was to investigate plastid DNA sequence diversity in a geographically diverse set of South Caucasian Vitis vinifera ssp. Sylvestris samples. DNA sequence diversity was investigated at three plastid regions (the trnH-psbA intergenic spacer, accD-psaI intergenic spacer and the rpl16 intron) in a group of 40 wild grape (Vitis vinifera ssp. Sylvestris) samples from the South Caucasus and at the same time complete plastid DNA sequence analysis of three Georgian wild grape samples were performed. Four plastid haplotypes were evident in the 40 samples, and are designated by their character states at each of the 4 polymorphic positions: AAAT, ATTT, GTAC and ATAT. Each haplotype has specific geographic distribution in the Caucasus region. Three Georgian wild grape samples from haplotype AAAT were subjected to complete chloroplast DNA Illumina sequencing. Sequence data analyses revealed complete identities between the sequences of AAAT haplotype wild grapes and the reference - Georgian cultivar 'Rkatsiteli' (V. Vinifera ssp. Vinifera), except for one sample where two 4-bp long inversions were detected. These observations highlight both unique and high levels of genetic variation in wild grapes (V. Vinifera ssp. Sylvestris) from the South Caucasus region and underlines their importance in the process of grape domestication in general. © 2015 ISHS. Source

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