Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes

Abstract

The genome sequence of the Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, is reported. With 1,191,693 nt in length and 1,023 predicted protein-coding genes, the Mamavirus has the largest genome among the known viruses. The genomes of the Mamavirus and the previously described Mimivirus are highly similar in both the protein-coding genes and the intergenic regions. However, the Mamavirus contains an extra 5'-terminal segment that encompasses primarily disrupted duplicates of genes present elsewhere in the genome. The Mamavirus also has several unique genes including a small regulatory polyA polymerase subunit that is shared with poxviruses. Detailed analysis of the protein sequences of the two Mimiviruses led to a substantial amendment of the functional annotation of the viral genomes.

FIG. 1.—

Schematic representation of the genome alignment of the Mamavirus and APMV. (A) The distributions of unaligned regions (longer than 200 nt, >20 nt gaps) in the Mamavirus and Mimivirus genomes. (B) The mean fraction of mismatches in aligned regions.

FIG. 2.—

The unique 5′-terminal fragment of the Mamavirus genome: genome rearrangements and duplications. The figure shows a comparison of the 5′-end of the Mamavirus genome (middle) with the 5′-end of the APMV genome (top) and a downstream region that is conserved in both genomes (bottom; Mimivirus genomic positions 9500–18000). The genomic coordinates for all Mimivirus genes are shown. Shading shows homology between Mamavirus and APMV genes or domains.

FIG. 3.—

Phylogenetic tree of the small regulatory subunit of polyA polymerase. The maximum-likelihood tree was constructed using TreeFinder (WAG matrix,G[Optimum]:4, 1,000 replicates, Search Depth 2; Jobb et al. 2004). The bootstrap support (expected-likelihood Weights) is shown for selected branches (percent). For each sequence, the species name abbreviation and the gene identification numbers are indicated; env stands for “marine metagenome.” Species abbreviations: Ec_Parte, Paramecium tetraurelia strain d4-2; Ec_Perma, Perkinsus marinus ATCC 50983; Ek_Leibr, Leishmania braziliensis MHOM/BR/75/M2904; Ek_Leiin, Leishmania infantum; Ek_Leima, Leishmania major strain Friedlin; Ek_Trybr, Trypanosoma brucei TREU927; Ek_Trycr, Trypanosoma cruzi strain CL Brener; El_Monbr, Monosiga brevicollis MX1; Eq_Naegr, Naegleria gruberi; u1_Bovpa, Bovine papular stomatitis virus; u1_Canvi, Canarypox virus; u1_Crovi, Crocodilepox virus; u1_Deevi, Deerpox virus W-1170-84; u1_Fowvi, Fowlpox virus; u1_Goavi, Goatpox virus Pellor; u1_Molco, Molluscum contagiosum virus subtype 1; u1_Myxvi, Myxoma virus; u1_Orfvi, Orf virus; u1_Swivi, Swinepox virus; u1_Tanvi, Tanapox virus; u1_Vacvi, Vaccinia virus; u2_Amsmo, Amsacta moorei entomopoxvirus “L”; u2_Melsa, Melanoplus sanguinipes entomopoxvirus.