Table 3.

Asymmetrically evolved duplicate gene pairs in A. fumigatus. ω_2,1 and ω_2,2 are variables of the selective pressure, class 2 of d_N/d_S, for two copies of duplicate genes in the branch-site model.

Gene pair	ω2,1	Systematic name	Functional description	ω2,2	Systematic name	Functional description	Portion of ω2 sites	P-value‡
1	>10	Afu1g10880	P-type calcium ATPase	>10	Afu3g10690	Calcium-translocating P-type ATPase	65.6%	<0.0001
2	>10	Afu1g00650†	Extracellular alpha-1,3-glucanase/mutanase	0.0263	Afu7g08510*	Extracellular alpha-1,3-glucanase/mutanase	61.8%	<0.0001
3	>10	Afu4g02720*	GPI anchored glycosyl hydrolase	0.00001	Afu3g00340	Glycosyl hydrolase	5.4%	<0.0001
4	>10	Afu8g04160	Folylpolyglutamate synthetase	0.00001	Afu6g09440	Tetrahydrofolylpolyglutamate synthase	4.0%	<0.0001
5	>10	Afu4g00860	Cell surface protein	0.00001	Afu6g12180	Conserved hypothetical protein	5.4%	<0.0001
6	>10	Afu1g00810*	Allergen Asp F7-like	0.00001	Afu4g06670	Allergen Asp f 7 Precursor	28.2%	<0.0001
7	>10	Afu1g05720	C-14 sterol reductase	0.2819	Afu1g03150	C-14 sterol reductase	4.0%	<0.0001
8	>10	Afu6g02240	ORF, Uncharacterized	0.1749	Afu3g03740*	Protein kinase	9.8%	<0.0001
9	5.7	Afu7g05110	Hypothetical protein	0.00001	Afu6g09410*	Conserved hypothetical protein	15.1%	<0.0001
10	5.1	Afu3g02420	ThiJ/PfpI family transcriptional regulator	0.00001	Afu4g01400	ThiJ/PfpI family protein	10.3%	<0.0001
11	3.4	Afu2g10840†	RTA1 domain protein	0.0183	Afu6g11810†	RTA1 domain protein	31.6%	<0.0001
12	4.1	Afu5g14920*	Hypothetical protein	0.0001	Afu5g07980	Hypothetical protein	19.8%	<0.0001
13	2.0	Afu7g08250*	C6 finger domain protein	0.00001	Afu2g08040	C6 finger domain protein	30.3%	<0.0001
14	1.2	Afu6g09300	C2H2 finger domain protein	0.0001	Afu4g14400†	C2H2 finger domain protein	18.5%	<0.0001
15	1.1	Afu1g01610	Conserved hypothetical protein	0.00001	Afu4g02880	Conserved hypothetical protein	34.5%	<0.001
16	0.0295	Afu5g11240	Oxidoreductase, short chain dehydrogenase/reductase family	0.0001	Afu6g09140	Oxidoreductase, short-chain dehydrogenase/reductase family	15.1%	<0.0001
17	0.0001	Afu3g15280	Methyltransferase	0.0000	Afu2g04380	LaeA-like methyltransferase	78.5%	<0.0001
18	0.0001	Afu5g14930*	Conserved hypothetical protein	0.0000	Afu1g16030*	Conserved hypothetical protein	8.5%	0.002
19	0.0001	Afu5g02410	ATP-dependent RNA helicase fal1	0.0000	Afu3g07200	DEAD/DEAH box RNA helicase	69.2%	0.004
20	0.0001	Afu4g10240	Small nuclear ribonucleoprotein SmD3	0.0000	Afu2g12020*	U6 snRNA-associated Sm-like protein LSM4	53.7%	0.007
21	1.8	Afu8g07150	Arsenic resistance protein ArsH	0.3139	Afu1g16120†	Arsenic resistance protein ArsH, flavoprotein	21.9%	0.009
22	0.2531	Afu6g07320	MFS multidrug transporter	0.1189	Afu6g09110	MFS multidrug transporter	31.1%	0.027
23	2.2	Afu5g14230*	C6 transcription factor	0.00001	Afu1g11290	Transcription regulator	6.2%	0.028
24	>10	Afu5g03930	Alcohol dehydrogenase	0.0001	Afu1g11020†	L-arabinitol 4-dehydrogenase	32.8%	0.047

Notes: The symbol

^*indicates negatively selected genes identified by using MKPRF; the symbol

^†indicates positively selected genes identified by using MKPRF. P values were obtained by likelihood ratio test between model ω_2,1 = ω_2,2 and ω_2,1 ≠ ω_2,2 (Materials and Methods).

^‡Duplicate genes with P < 0.0001 remain significant after Bonferroni correction.