Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.
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.
Hatfull
Graham F
GF
Department of Biological Sciences, Pittsburgh Bacteriophage Institute, Pittsburgh, PA 15260, USA. gfh@pitt.edu
Jacobs-Sera
Deborah
D
Lawrence
Jeffrey G
JG
Pope
Welkin H
WH
Russell
Daniel A
DA
Ko
Ching-Chung
CC
Weber
Rebecca J
RJ
Patel
Manisha C
MC
Germane
Katherine L
KL
Edgar
Robert H
RH
Hoyte
Natasha N
NN
Bowman
Charles A
CA
Tantoco
Anthony T
AT
Paladin
Elizabeth C
EC
Myers
Marlana S
MS
Smith
Alexis L
AL
Grace
Molly S
MS
Pham
Thuy T
TT
O'Brien
Matthew B
MB
Vogelsberger
Amy M
AM
Hryckowian
Andrew J
AJ
Wynalek
Jessica L
JL
Donis-Keller
Helen
H
Bogel
Matt W
MW
Peebles
Craig L
CL
Cresawn
Steven G
SG
Hendrix
Roger W
RW
D001483:Base Sequence; D016000:Cluster Analysis; D005814:Genes, Viral / Q000235:genetics*; D014644:Genetic Variation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D009160:Mycobacteriophages / Q000235:genetics* / Q000302:isolation & purification; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014771:Virion / Q000235:genetics
D009711:Nucleotides