. 2018 Jul 19;210(1):303–313. doi: 10.1534/genetics.118.301249

Table 1. Gene pairs for which the relative ages could be determined.

Accession number	Organism	Ancestral gene	Novel gene	Overlap length (n+)	Novel frame
NC_001401	Adeno-associated virus 2	VP2	AAP	615	+1
NC_004285	Aedes albopictus densovirus	NS1	NS2	1119	+1
NC_001467	African cassava mosaic virus	AL1	AC4	423	+1
NC_009896	Akabane virus^a	N	NSs	276	+1
NC_001749	Apple stem grooving virus	MP	Polyprotein	963	+1
NC_001719	Arctic ground squirrel hepatitis virus^b	P	L	1284	+1
NC_003481	Barley stripe mosaic virus^c^,^d^,^e	TGBp2	TGBp3	191	+1
NC_003680	Barley yellow dwarf virus^f^,^g	P5	MP	465	+1
NC_005041	Blattella germanica densovirus	NS-1	ORF4	789	+1
NC_001927	Bunyamwera virus^a	N	NSs	306	+1
NC_001658	Cassava common mosaic virus^d^,^e	TGBp2	TGBp3	152	+1
NC_001427	Chicken anemia virus	VP2	Apoptin	366	+1
NC_003688	Cucurbit aphid-born yellowing virusi^f^,^g^,^h	CP	P5	572	+1
NC_005899	Dendrolimus punctatus Tetravirus^f	p71	p17	381	+1
NC_016561	hepatitis B^b	P	L	1128	+1
NC_003608	Hibiscus chlorotic ringspot virus^f	Coat	p25	675	+1
NC_003608	Hibiscus chlorotic ringspot virus	Replicase	p23	630	+1
NC_004730	Indian peanut clump virus	P14	P17	158	+1
KR732417	Influenza A virus H5N1	PB1	PB1-F2	273	+1
NC_009025	Israel acute paralysis virus of bees	ORF2	ORFx	285	+1
NC_003627	Maize chlorotic mottle virus	Coat	³¹P	451	+1
NC_001498	Measles virusⁱ	P	C	561	+1
NC_005339	Mossman virusⁱ	P	C	459	+1
NC_008311	Murine norovirus	VP1	VF1	642	+1
NC_001633	Mushroom bacilliform virus	ORF1	Vpg-protease	533	+1
NC_001718	Porcine parvovirus	Capsid	SAT	207	+1
NC_001747	Potato leafroll virus	P0	P1	661	+1
NC_003725	Potato mop-top virus^c^,^d	TGBp2	TGBp2	146	+1
NC_003768	Rice dwarf virus	Pns12	OP-ORF	276	+1
NC_003771	Rice ragged stunt virus	P4b	Replicase	981	+1
NC_004718	SARS coronavirus	Nucleocapsid	Protein I	297	+1
NC_003809	Spinach latent virus	Replicase	2b	308	+1
NC_003448	Striped Jack nervous necrosis virus	Protein A	B2	228	+1
NC_001366	Theiler’s virus	L	L*	471	+1
NC_002199	Tupaia paramyxovirusⁱ	P	C	462	+1
NC_003743	Turnip yellows virus^f^,^g^,^h	CP	ORF5	528	+1
NC_001409	Apple chlorotic leaf spot virus	CP	MP	317	+2
NC_001719	Arctic ground squirrel hepatitis virus	P	Capsid Precursor	158	+2
NC_001719	Arctic ground squirrel hepatitis virus	P	X	256	+2
NC_003532	Cymbidium ringspot virus	MP	p19	519	+2
NC_003093	Indian citrus ringspot virus	CP	NABP	301	+2
NC_004178	Infectious bursal disease virus^j	VP2	VP5	404	+2
NC_001915	Infectious pancreatic necrosis virus^j	VP2	VP5	395	+2
NC_001990	Nudaurelia capensis beta virus^f	CP	Replicase	1832	+2
NC_014126	Providence virus	p104	p130	2681	+2
NC_004366	Tobacco bushy top virus	MP	RNP	698	+2
NC_004063	Turnip yellows mosaic virus	Replicase	MP	1880	+2

Genes are phylogenetically independent except as noted in the footnotes.

N/NSs overlaps share $\geq 50 %$ sequence similarity.

P/L overlap predicted homologous in HMMer run.

TGBp2 genes share $\geq 50 %$ protein sequence similarity.

TGBp2 genes predicted homologous Morozov and Solovyev (2003).

TGBp3 genes predicted homologous Morozov and Solovyev (2003).

Ancestral genes predicted homologous in HMMer run.

Novel genes predicted homologous in HMMer run.

ⁱ

Novel genes predicted homologous in HMMer run.

Ancestral VP2 genes share $\geq 50 %$ protein sequence similarity.