Complete Genomic Sequence of the Virulent Salmonella Bacteriophage SP6

ABSTRACT We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is ∼5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.

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Isolation and characterization of the rye Waxy gene

Genome ◽

10.1139/g09-036 ◽

2009 ◽

Vol 52 (7) ◽

pp. 658-664 ◽

Cited By ~ 5

Author(s):

Jie Xu ◽

Michele Frick ◽

André Laroche ◽

Zhong-Fu Ni ◽

Bao-Yun Li ◽

...

Keyword(s):

Genomic Sequence ◽

Evolutionary Relationship ◽

Waxy Gene ◽

Coding Region ◽

Gene Encoding ◽

Sequence Comparisons ◽

Cdna Sequences ◽

Isolation And Characterization ◽

Complete Genomic

Complete genomic and cDNA sequences of the Waxy gene encoding granule-bound starch synthase I (GBSSI) were isolated from the rye genome and characterized. The full-length rye Waxy genomic DNA and cDNA are 2767 bp and 1815 bp, respectively. The genomic sequence has 11 exons interrupted by 10 introns. The rye Waxy gene is GC-rich, with a higher GC frequency in the coding region, especially in the third position of the codons. Exon regions of the rye Waxy gene are more conserved than intron regions when compared with the homologous sequences of other cereals. The mature rye GBSSI proteins share more than 95% sequence identity with their homologs in wheat and barley. A phylogenetic tree based on sequence comparisons of available plant GBSSI proteins shows the evolutionary relationship among Waxy genes from rye and other plant genomes. The identification of the rye Waxy gene will enable the manipulation of starch metabolism in rye and triticale.

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Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome

Journal of Bacteriology ◽

10.1128/jb.01233-09 ◽

2009 ◽

Vol 192 (2) ◽

pp. 560-567 ◽

Cited By ~ 131

Author(s):

Tyler Jarvik ◽

Chris Smillie ◽

Eduardo A. Groisman ◽

Howard Ochman

Keyword(s):

Salmonella Enterica ◽

Salmonella Enterica Serovar Typhimurium ◽

Genomic Sequence ◽

Genetic Alterations ◽

Sequence Evolution ◽

Complete Genomic Sequence ◽

Short Term ◽

Typhimurium Strain ◽

Serovar Typhimurium ◽

Complete Genomic

ABSTRACT Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for the disease promoted by the human-adapted S. enterica serovar Typhi. Despite its health importance, the only S. Typhimurium strain for which the complete genomic sequence has been determined is the avirulent LT2 strain, which is extensively used in genetic and physiologic studies. Here, we report the complete genomic sequence of the S. Typhimurium strain 14028s, as well as those of its progenitor and two additional derivatives. Comparison of these S. Typhimurium genomes revealed differences in the patterns of sequence evolution and the complete inventory of genetic alterations incurred in virulent and avirulent strains, as well as the sequence changes accumulated during laboratory passage of pathogenic organisms.

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Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽

10.3390/genes12081212 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1212

Author(s):

J. Spencer Johnston ◽

Carl E. Hjelmen

Keyword(s):

Next Generation Sequencing ◽

Genetic Basis ◽

Genomic Sequence ◽

Sequence Data ◽

Complete Genomic Sequence ◽

Special Issue ◽

Model Species ◽

Road Map ◽

Generation Sequencing ◽

Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

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