Dataset Information

Characterization of the genome, proteome, and structure of yersiniophage ?R1-37.

ABSTRACT: The bacteriophage vB_YecM-?R1-37 (?R1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ?R1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ?R1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ?R1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ?KZ. The tail of ?R1-37 has a contractile sheath. We conclude that phage ?R1-37 is a representative of a novel phage type that carries the dU-containing genome in a ?KZ-like head.

SUBMITTER: Skurnik M

PROVIDER: S-EPMC3497697 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37.

Skurnik Mikael M Hyytiäinen Heidi J HJ Happonen Lotta J LJ Kiljunen Saija S Datta Neeta N Mattinen Laura L Williamson Kirsty K Kristo Paula P Szeliga Magdalena M Kalin-Mänttäri Laura L Ahola-Iivarinen Elina E Kalkkinen Nisse N Butcher Sarah J SJ

Journal of virology 20120912 23

The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ϕR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. T ...[more]

PMID: 22973030

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Project description:BackgroundNumerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties.ResultsAverage genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions.ConclusionsOur results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies.

Dataset Information

Characterization of the genome, proteome, and structure of yersiniophage ?R1-37.

Publications

Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37.

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