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Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size

Hatfull, GF and Jacobs-Sera, D and Lawrence, JG and Pope, WH and Russell, DA and Ko, CC and Weber, RJ and Patel, MC and Germane, KL and Edgar, RH and Hoyte, NN and Bowman, CA and Tantoco, AT and Paladin, EC and Myers, MS and Smith, AL and Grace, MS and Pham, TT and O'Brien, MB and Vogelsberger, AM and Hryckowian, AJ and Wynalek, JL and Donis-Keller, H and Bogel, MW and Peebles, CL and Cresawn, SG and Hendrix, RW (2010) Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size. Journal of Molecular Biology, 397 (1). 119 - 143. ISSN 0022-2836

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Abstract

Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. Of the 60 phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, 5 of which can be further divided into subclusters; 5 genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. In contrast, similarity between the 2 genomes in Cluster I is barely detectable by diagonal plot analysis. In total, 6858 predicted open-reading frames have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries, and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains. © 2010 Elsevier Ltd. All rights reserved.


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Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Hatfull, GFgfh@pitt.eduGFH
Jacobs-Sera, Ddjs@pitt.eduDJS0000-0001-7838-3257
Lawrence, JGjlawrenc@pitt.eduJLAWRENC
Pope, WH
Russell, DAdar78@pitt.eduDAR780000-0001-6894-2748
Ko, CC
Weber, RJ
Patel, MC
Germane, KL
Edgar, RH
Hoyte, NN
Bowman, CA
Tantoco, AT
Paladin, EC
Myers, MS
Smith, AL
Grace, MS
Pham, TT
O'Brien, MB
Vogelsberger, AM
Hryckowian, AJ
Wynalek, JL
Donis-Keller, H
Bogel, MW
Peebles, CLcpeebles@pitt.eduCPEEBLES0000-0001-7938-3312
Cresawn, SG
Hendrix, RWrhx@pitt.eduRHX
Date: 19 March 2010
Date Type: Publication
Journal or Publication Title: Journal of Molecular Biology
Volume: 397
Number: 1
Page Range: 119 - 143
DOI or Unique Handle: 10.1016/j.jmb.2010.01.011
Schools and Programs: Dietrich School of Arts and Sciences > Biological Sciences
Refereed: Yes
ISSN: 0022-2836
MeSH Headings: Base Sequence; Cluster Analysis; Genes, Viral--genetics; Genetic Variation; Molecular Sequence Data; Multigene Family--genetics; Mycobacteriophages--genetics; Mycobacteriophages--isolation & purification; Nucleotides--genetics; Open Reading Frames--genetics; Phylogeny; Sequence Alignment; Sequence Analysis, DNA; Virion--genetics
Other ID: NLM NIHMS170242, NLM PMC2830324
PubMed Central ID: PMC2830324
PubMed ID: 20064525
Date Deposited: 15 Nov 2012 20:36
Last Modified: 31 Jul 2020 15:56
URI: http://d-scholarship.pitt.edu/id/eprint/16240

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