Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae)

Table 2 Comparison of various methods to identify tRNAs in the Solenopsis mitogenomes.

		geminata			Richteri			PMS			VMS
		DOGMA	tRNAscan	ARWEN	DOGMA	tRNAscan	ARWEN	DOGMA	tRNAscan	ARWEN	DOGMA	tRNAscan	ARWEN
tRNA Type	Anti Codon	Cove score	Cove Score		Cove score	Cove Score		Cove score	Cove Score		Cove score	Cove Score
L₂	TAA	47.63	22.63	yes	49.15	31.79	yes	49.15	31.79	yes	49.15	31.06	yes
K	TTT	44.74	18.29	yes	39.21	21.78	yes	39.21	21.78	yes	37.64	21.78	yes
D	GTC	47.83	24.42	yes	41.13	18.89	yes	42.77	18.09	yes	42.79	18.9	yes
G	TCC	58.63	36.52	yes	49.5	32.45	yes	51.34	29.97	yes	48.23	29	yes
A	TGC	46.06	19.45	yes	48.9	24.57	yes	48.9	24.57	yes	54.71	25.98	yes
R	TCG	45.47	19.34	yes	39.41	---	yes	39.41	---	yes	38.96	---	yes
S₁	TCT	---	---	---	26.43	---	yes	26.43	---	yes	27.89	---	---
E	TTC	53.66	25.17	yes	52.91	24.39	yes	52.91	24.39	yes	52.91	24.39	yes
F	GAA	46.74	30.61	yes	38.05	24.63	yes	38.49	28.14	yes	38.26	---	yes
H	GTG	54.21	20.57	yes	43.51	18.42	yes	43.51	18.42	yes	43.51	18.42	yes
T	TGT	58.18	27.74	yes	53.59	29.42	yes	53.59	29.42	yes	58.58	24.55	yes
P	TGG	51.68	26.94	yes	56.84	22.42	yes	56.84	22.42	yes	59.46	25.1	yes
S₂	TGA	48.14	20.98	yes	48.14	20.98	yes	48.14	20.98	yes	48.14	20.98	yes
L ₁	TAG	25.07	18.66	yes	19.23	17.8	---	20.18	18.97	yes	---	16.85	yes
N	ATT	25.55	15.34	---	32.4	---	---	32.4	---	yes	---	---	---
V	TAC	48.34	18.03	yes	59.55	33.94	yes	59.55	33.94	yes	55.58	31.31	yes
M	CAT	42.75	18.84	yes	44.28	15.68	yes	43.92	---	yes	42.53	20.11	yes
I	GAT	36.35	---	yes	36.59	15.13	yes	36.18	19.8	yes	37.02	21.35	yes
Q	TTG	53.61	42.39	yes	51.22	41.64	yes	51.22	41.64	yes	53.25	42.31	yes
W	TCA	52.16	27.57	yes	47.34	30.06	yes	48.69	27.06	yes	44.83	26.98	yes
C	GCA	56.88	28.08	yes	61.16	27.44	yes	57.83	26.43	yes	57.44	28.93	yes
Y	GTA	44.94	20.78	yes	46.2	26.86	yes	43.75	24.44	yes	47	24.81	yes

DOGMA and ARWEN generally overpredicted tRNAs (data not shown) and tRNAscan underpredicted tRNA loci. COVE scores >20 are generally considered to indicate reliable identification of tRNAs. Some tRNAs were readily identified by all methods, whereas some proved harder to identify and had to be manually folded in some mitogenomes (e.g., tRNA-S₁). Loci underlined are located on the N strand.

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