Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids

Boyd, Bret M.; Chevignon, Germain; Patel, Vilas; Oliver, Kerry M.; Strand, Michael R.

doi:10.1186/s12985-021-01685-y

Virology Journal

Table 2 Best hits identified to APSE3 AS3 coding sequences in other sequenced viruses or bacteria

From: Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids

Module	Locus	Alternative locus	Protein	Translation	Translation	BLASTP target: sequenced	Viral	Amino acid	BLASTP Target: sequenced γ-proteobacteria	Amino acid	BLASTP Target: all other	Amino acid
Module	Tag	Tag	Description	Start	Stop	viruses	family	Identity	That are insect symbionts	Identity	sequenced γ-proteobacteria	Identity
1	P38	APACPISMAS3_01	Integrase	1243	71	Proteus phage NV18	Podoviridae	76.68	Arsenophonus sp. ENCA	96.15	Hafnia alvei	73.78
1	P40	APACPISMAS3_02	Excisionase	1479	1099	Salmonella phage epsilon34	Podoviridae	44.72	Sodalis glossinidius	25	Morganella morganii	60
1	P41	APACPISMAS3_03	Dead-box helicase	2993	1611	Yersinia phage YeP4	Podoviridae	66.09	Ca. Arsenophonus triatominarum	93.9	Providencia alcalifaciens	81.4
1	P42	APACPISMAS3_04	DNA binding protein Roi	3744	3013	Cronobacter phage ENT47670	Siphoviridae	40.16	Serratia symbiotica str. Tucson	33.33	Xenorhabdus sp. PB62.4	54.58
1	P43	APACPISMAS3_05	Antirepressor	4591	3809	Salmonella phage SPN3UB	Siphoviridae	36.78	Arsenophonus nasoniae	87.31	Salmonella enterica	48.47
1	P44	APACPISMAS3_08	Nuclease	5166	4885	Xylella phage Xfas53	Podoviridae	43.01	Arsenophonus nasoniae	95.7	Morganella morganii	78.65
1	P45	APACPISMAS3_10	DNA polymerase I	7464	5401	Yersinia phage YeP4	Podoviridae	62.64	Arsenophonus sp. ENCA	92.87	Vibrio vulnificus	76.79
1	P46	APACPISMAS3_11	Transcriptional regulator	7809	7477	Escherichia phage D6	Myoviridae	30.53	Arsenophonus nasoniae	90	Xenorhabdus sp.	72.46
1	P47	APACPISMAS3_12	Phage protein	7900	8394	Xylella phage Xfas53	Podoviridae	37.3	Ca. Symbiopectobacerium PLON1	76.22	Erwinia tracheiphila	46.76
1	P49	APACPISMAS3_14	Phage protein	8685	8413	NA	NA	NA	Arsenophonus nasoniae	76.47	NA	NA
1	P50	APACPISMAS3_15	Phage protein	9308	8754	Yersinia phage YeP4	Podoviridae	59.02	Arsenophonus sp. Aphis craccivora	90.76	Proteus mirabilis	68.31
1	P51	APACPISMAS3_16	Phage protein	10,622	9324	Yersinia phage YeP4	Podoviridae	54.93	Arsenophonus nasoniae	89.58	Vibrio vulnificus	62.3
1	P53	APACPISMAS3_17	Phage protein	11,538	10,615	Yersinia phage YeP4	Podoviridae	34.05	Arsenophonus sp. Aleurodicus floccissimus	75.16	Providencia alcalifaciens	40.6
2	P1	APACPISMAS3_18	Repressor	12,804	12,106	Yersinia phage YeP4	Podoviridae	47.11	Arsenophonus sp. Aleurodicus floccissimus	89.66	Citrobacter koseri	50.22
2	P2	N/A	Transcriptional regulator	12,900	13,184	Yersinia phage YeP4	Podoviridae	57.89	Arsenophonus sp. Aleurodicus floccissimus	80.85	Izhakiella capsodis	42.05
2	P3	APACPISMAS3_20	ATPase	13,188	15,461	Yersinia phage YeP4	Podoviridae	67.89	Arsenophonus sp. Aleurodicus floccissimus	91.15	Providencia alcalifaciens	70.13
2	P5	APACPISMAS3_21	Antitermination protein Q	15,889	16,335	Stx2a-converting phage Stx2	Siphoviridae	61.67	Arsenophonus sp. Aphis craccivora	95.95	Escherichia coli	58.22
3	Toxin	APACPISMAS3_23*	YD-repeat protein	17,764	22,185	NA	NA	NA	Arsenophonus sp. Aleurodicus floccissimus	65.77	Raoultella terrigena	56.18
3	Toxin	APACPISM5AT_28*	cdtB	19,883	20,872	Enterobacteria phage cdtl	Siphoviridae	27.91	Arsenophonus sp. Bemesia tabaci	48.6	Avibacterium paragallinarum	29.91
3	Toxin	APACPISM1_23*	stxB	5398	6498	NA	NA	NA	NA	NA	Photorhabdus sp.	23.58
3	K	APACPISMAS3_24	Group II holin	22,837	23,028	Morganella phage IME1369_02	Siphoviridae	34.29	Arsenophonus sp. Bemesia tabaci	75.44	Photorhabdus luminescens	52.63
3	F	APACPISMAS3_25	Lysozyme	23,018	23,491	Salmonella virus BTP1	Podoviridae	52.15	Arsenophonus sp. Bemesia tabaci	85.99	Serratia marcescnes	56.34
3	P14	APACPISMAS3_26*	Exported protein	23,487	23,882	Enterobacteria phage SfV	Myoviridae	12.5	Arsenophonus sp. Bemesia tabaci	88.2	Pantoea ananatis	32.82
3	P16	N/A	Endolysin	23,911	24,030	Klebsiella phage ST16-OXA48phi5.4	Myoviridae	48.72	Arsenophonus sp. Bemesia tabaci	97.44	Xenothabdus vietnamensis	70.27
4	P17	APACPISMAS3_27*	Terminase, small	24,104	24,517	Providencia phage PSTNGR2lys	Siphoviridae	79.05	Arsenophonus nasoniae	89.71	Providencia stuartii	80.95
4	P18	APACPISMAS3_28	Terminase, large	24,534	25,934	Shigella virus Sf6	Podoviridae	38.7	Ca. Arsenophonus triatominarum	91.24	Thiolinea disciformis	54.2
4	P19	APACPISMAS3_29	Portal protein	25,940	28,105	Shigella virus Sf6	Podoviridae	70.9	Ca. Arsenophonus triatominarum	88.97	Providencia alcalifaciens	87.99
4	P23	APACPISMAS3_30	Scaffolding protein	28,156	29,052	Shigella virus Sf6	Podoviridae	58.94	Arsenophonus nasoniae	79.53	Providencia rettgeri	72.24
4	P24	APACPISMAS3_31	Major capsid protein	29,063	30,334	Salmonella virus HK620	Podoviridae	79.2	Ca. Arsenophonus triatominarum	93.6	Providencia alcalifaciens	85.07
4	P27	APACPISMAS3_33	DNA stabilization protein	30,554	31,036	Salmonella virus HK620	Podoviridae	58.13	Ca. Arsenophonus triatominarum	82.5	Providencia rettgeri	77.78
4	P28	APACPISMAS3_34	DNA stabilization protein	31,008	32,423	Salmonella phage SPN9CC	Podoviridae	60.81	Arsenophonus nasoniae	83.65	Morganella sp.	63.56
4	P30	APACPISMAS3_35	DNA stabilization protein	32,423	32,779	Proteus phage NV18	Podoviridae	38.79	Arsenophonus sp. Aleurodicus floccissimus	49.38	Providencia alcalifaciens	42.86
4	P31	APACPISMAS3_36	Hypothetical protein	32,779	33,246	Proteus phage NV18	Podoviridae	36.3	Arsenophonus sp. Aleurodicus floccissimus	84.52	Proteus mirabilis	35.95
4	P32	APACPISMAS3_37	DNA transfer protein	33,224	33,853	Escherichia phage vB EcoP Kapi1	Podoviridae	63.24	Arsenophonus sp. Aleurodicus floccissimus	82.16	Escherichia coli	63.55
4	P33	APACPISMAS3_38	DNA transfer protein	33,866	35,254	Salmonella virus BTP1	Podoviridae	33.13	Arsenophonus sp. Aleurodicus floccissimus	83.69	Salmonella enterica	65.34
4	P35	APACPISMAS3_39	DNA transfer protein	35,254	37,131	Salmonella virus P22	Podoviridae	64.03	Arsenophonus sp. Aleurodicus floccissimus	87.28	Klebsiella pneumoniae	68.43
4	P36	APACPISMAS3_40	Tail fiber protein	37,160	38,179	Proteus phage NV18	Podoviridae	72.27	Arsenophonus nasoniae	67.34	Proteus mirabilis	74.36
4	P37	APACPISMAS3_41*	Tail fiber assembly protein	38,158	38,625	Shigella phage SfIV	Myoviridae	32.37	Arsenophonus nasoniae	72.26	Acinetobacter baumannii	50.34

Each predicted coding sequence in the APSE3 AS3 genome, along with stxB and cdtB genes from APSE1 and APSE8 5AT, were used to search using BLASTp all submitted genomes for Caudoviruses and γ-proteobacteria that are either insect symbionts or not insect symbionts
*Denotes differences in predicted transcriptional start and stop exist between annotations of APSE

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ISSN: 1743-422X

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