Archaea / 2013 / Article / Tab 5

Research Article

PH1: An Archaeovirus of Haloarcula hispanica Related to SH1 and HHIV-2

Table 5

Main differences (divergent regions) between the SH1 and PH1 genomes.

RegionaSH1 startbSH1 stopLength (bp)PH1 startPH1 stopLength (bp)Comment

DV152765012353860466Replacement. Both regions have direct repeats at their borders; PH1 has two sets GACCCGGC and CGCTGC, while SH1 has CCCGAC. In SH1, this replacement region includes the C-terminal region of ORF2 and the N-terminal region of ORF3. In PH1, it covers only the C-terminal region of ORF1

DV22433258815523862387RMDc from PH1. SH1 repeat at border is TGACCG. This removes the homolog of SH1 ORF10 from PH1

DV33324359827431373416279Replacement at the beginning of SH1 ORF13/PH1 ORF12 (capsid protein VP1)

DV46656712847264787085607Replacement near the C-terminus of SH1 ORF13/PH1 ORF12 (capsid protein VP1)

DV57491834185074467447Indel that results in ORFs14-16 of SH1 not being present in PH1. SH1 ORF14 has a close homolog in HHIV-2 (ORF6), in a similar position, just after the VP1 homolog. SH1 ORF15 is a conserved protein in haloarchaea (e.g. NP_2552A, and Hmuk_2978) and halovirus His1 (ORF13). Possible inverted repeat (AGCCATG) at border of SH1 region

DV61370513706128181285133RMD from SH1. PH1 repeat at border is CAGCGG(g/t)G. This removes a part of capsid protein VP2 sequence from the SH1 protein

DV713789138637412934129417Replacement. This occurs within VP2 gene of both viruses

DV81514215186441422014221RMD from PH1. SH1 repeat at border is TG(t/c)CCGACGA and occurs within capsid protein VP2 gene of both viruses

DV91530315317141433714338RMD from PH1. SH1 repeat at border is GCCGACGA and occurs within capsid protein VP2 gene of both viruses

DV101550415527231452914530RMD from PH1. SH1 repeat at border is GACGA and occurs within capsid protein VP2 of both viruses

DV1120026204053791901919173154Replacement beginning at the start of SH1 ORF35/PH1 ORF31. This region is longer in SH1, where it includes ORF36, an ORF that has no homolog present in PH1

DV122044020661221192081928678Replacement. This is unequal and includes an ORF in SH1 (ORF38) that is not present in PH1

DV1320943210851421956219728166Replacement. This covers SH1 ORF40/PH1 ORF34. The predicted proteins are not homologous

DV142354123542221712219727Probable RMD in SH1. PH1 repeat at border is CGTCTCGG and occurs in SH1 ORF44/PH1 ORF38

DV152450624521152315223153Probable RMD in PH1. SH1 repeat at border is CTCGGT and occurs near the end of SH1 ORF45/PH1 ORF39

DV162495124964132357923580Probable RMD in PH1. SH1 repeat at border is CGGTC and occurs in SH1 ORF47/PH1 ORF41

DV1726449264502505025274224Probable RMD in SH1. PH1 repeat at border is TCATGCG and occurs near the start of SH1 ORF50/PH1 ORF44 and provides an extra ORF for PH1 (ORF45)

DV18270742976469025895269331038Replacement. Left border at start of SH1 ORF51/PH1 ORF47 and extends rightwards into SH1 ORF55/PH1 ORF49 (VP18 gene). It is an unequal replacement and SH1 has two more ORFs in this region than PH1

DV: Divergent regions between the genomes of SH1 and PH1.
Start and stop positions refer to the GenBank sequences of the two viruses: SH1, NC_007217.1; PH1, KC252997.
RMD: repeat-mediated deletion event, as described in [20].