Archaea

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.


Region^a	SH1 start^b	SH1 stop	Length (bp)	PH1 start	PH1 stop	Length (bp)	Comment

DV1	527	650	123	538	604	66	Replacement. 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

DV2	2433	2588	155	2386	2387	—	RMD^c from PH1. SH1 repeat at border is TGACCG. This removes the homolog of SH1 ORF10 from PH1

DV3	3324	3598	274	3137	3416	279	Replacement at the beginning of SH1 ORF13/PH1 ORF12 (capsid protein VP1)

DV4	6656	7128	472	6478	7085	607	Replacement near the C-terminus of SH1 ORF13/PH1 ORF12 (capsid protein VP1)

DV5	7491	8341	850	7446	7447	—	Indel 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

DV6	13705	13706	—	12818	12851	33	RMD from SH1. PH1 repeat at border is CAGCGG(g/t)G. This removes a part of capsid protein VP2 sequence from the SH1 protein

DV7	13789	13863	74	12934	12941	7	Replacement. This occurs within VP2 gene of both viruses

DV8	15142	15186	44	14220	14221	—	RMD from PH1. SH1 repeat at border is TG(t/c)CCGACGA and occurs within capsid protein VP2 gene of both viruses

DV9	15303	15317	14	14337	14338	—	RMD from PH1. SH1 repeat at border is GCCGACGA and occurs within capsid protein VP2 gene of both viruses

DV10	15504	15527	23	14529	14530	—	RMD from PH1. SH1 repeat at border is GACGA and occurs within capsid protein VP2 of both viruses

DV11	20026	20405	379	19019	19173	154	Replacement 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

DV12	20440	20661	221	19208	19286	78	Replacement. This is unequal and includes an ORF in SH1 (ORF38) that is not present in PH1

DV13	20943	21085	142	19562	19728	166	Replacement. This covers SH1 ORF40/PH1 ORF34. The predicted proteins are not homologous

DV14	23541	23542	—	22171	22197	27	Probable RMD in SH1. PH1 repeat at border is CGTCTCGG and occurs in SH1 ORF44/PH1 ORF38

DV15	24506	24521	15	23152	23153	—	Probable RMD in PH1. SH1 repeat at border is CTCGGT and occurs near the end of SH1 ORF45/PH1 ORF39

DV16	24951	24964	13	23579	23580	—	Probable RMD in PH1. SH1 repeat at border is CGGTC and occurs in SH1 ORF47/PH1 ORF41

DV17	26449	26450	—	25050	25274	224	Probable 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)

DV18	27074	29764	690	25895	26933	1038	Replacement. 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].