PH1: An Archaeovirus of Haloarcula hispanica Related to SH1 and HHIV-2
Genome alignments of haloviruses PH1, SH1, and HHIV-2, along with two related genomic loci. (a) Genomic loci of Hap. paucihalophilus and Hbf. lacisalsi that contain genes related to halosphaeroviruses SH1, PH1, and HHIV-2. The names and GenBank accessions for these contigs are given on the far right, and ORFs are coloured and labeled to indicate the relationships of these ORFs to those of the viruses below. The locus tag numbers for the first and last ORFs shown in each locus are given nearby their respective ORFs. In addition, grey coloured ORFs represent sequences that do not match any of the haloviruses, and green coloured ORFs represent protein sequences that are closely related to ORFs found within or very close to previously described virus/plasmid loci, so called ViPREs . The scale bars shown above each contig show the position of the described region within the respective contig. (b) The three virus genomes are labeled at the left, with scale markers below (in kb) and the total length indicated at the far right. At the bottom is a cumulative AT-skew plot of the PH1 genome (http://molbiol-tools.ca/Jie_Zheng/), with inflection points circled. The grey shaded bands between the genome diagrams indicate significant nucleotide similarity (using ACT ). Annotated ORFs are represented by arrows, with colours indicating structural proteins (red or brown), nonstructural proteins (yellow or orange) or the packaging ATPase (blue). The names of structural protein ORFs are indicated either within the arrow (e.g., VP1) or in text nearby. The numbered, orange coloured ORFs of HHIV-2 are homologous to ORFs found in the genomic loci (probably proviruses or provirus remnants) pictured in (a).