Comparative analysis of the complete mitochondrial genomes of related species Chrysolophus amherstiae and Chrysolophus pictus

Figures & data

Table 1. Annotation of the mitochondrial genome of Chrysolophus amherstiae (C.a) and Chrysolophus pictus (C.p).

Gene	Direction	Direction	Nucleotide number		Size (bp)		IGS (bp)		Anticodon	Start codon	Stop codon
			C.a	C.p	C.a	C.p	C.a	C.p
D-loop	+	H	1–1150	1–1148	1150	1148
tRNA-Phe	+	H	1151–1218	1149–1216	68	68	0	0	GAA
12S rRNA	+	H	1218–2186	1216–2184	969	969	–1	–1
tRNA-Val	+	H	2187–2259	2185–2257	73	73	0	0	TAC
16S rRNA	+	H	2260–3865	2258–3862	1606	1605	0	0
tRNA-Leu^(UUR)	+	H	3865–3938	3862–3935	74	74	–1	–1	TAA
ND1	+	H	3950–4924	3947–4921	975	975	11	11		ATG	TAA
tRNA-Ile	+	H	4925–4996	4922–4993	72	72	0	0	GAT
tRNA-Gln	–	L	5003–5073	5000–5070	71	71	6	6	TTG
tRNA-Met	+	H	5073–5141	5070–5138	69	69	–1	–1	CAT
ND2	+	H	5142–6180	5139–6177	1039	1039	0	0		ATG	T--
tRNA-Trp	+	H	6181–6256	6178–6253	76	76	0	0	TCA
tRNA-Ala	–	L	6262–6330	6260–6328	69	69	5	6	TGC
tRNA-Asn	–	L	6334–6406	6332–6404	73	73	3	3	GTT
tRNA-Cys	–	L	6409–6475	6407–6473	67	67	2	2	GCA
tRNA-Tyr	–	L	6475–6545	6473–6543	71	71	–1	–1	GTA
COXI	+	H	6547–8097	6545–8095	1551	1551	1	1		GTG	AGG
tRNA-Ser^(UCN)	–	L	8089–8163	8087–8161	75	75	–9	–9	TGA
tRNA-Asp	+	H	8166–8234	8164–8232	69	69	2	2	GTC
COXII	+	H	8236–8919	8234–8917	684	684	1	1		ATG	TAA
tRNA-Lys	+	H	8921–8988	8919–8986	68	68	1	1	TTT
ATP8	+	H	8990–9154	8988–9152	165	165	1	1		ATG	TAA
ATP6	+	H	9145–9828	9143–9826	684	684	–10	–10		ATG	TAA
COXIII	+	H	9828–10611	9826–10609	784	784	–1	–1		ATG	T--
tRNA-Gly	+	H	10612–10680	10610–10678	69	69	0	0	TCC
ND3	+	H	10681–11032	10679–11030	352	352	0	0		ATG	TAA
tRNA-Arg	+	H	11034–11102	11032–11100	69	69	1	1	TCG
ND4L	+	H	11103–11399	11101–11397	297	297	0	0		ATG	TAA
ND4	+	H	11393–12770	11391–12768	1378	1378	–7	–7		ATG	T--
tRNA-His	+	H	12771–12839	12769–12837	69	69	0	0	GTG
tRNA-Ser^(AGN)	+	H	12841–12906	12839–12904	66	66	1	1	GCT
tRNA-Leu^(CUN)	+	H	12906–12976	12905–12975	71	71	–1	0	TAG
ND5	+	H	12977–14794	12976–14793	1818	1818	0	0		ATG	TAA
CYTB	+	H	14799–15941	14798–15940	1143	1143	4	4		ATG	TAG
tRNA-Thr	+	H	15943–16011	15942–16010	69	69	1	1	TGT
tRNA-Pro	–	L	16014–16082	16013–16081	69	69	2	2	TGG
ND6	–	L	16089–16610	16088–16609	522	522	6	6		ATG	TAG
tRNA-Glu	–	L	16612–16679	16611–16678	68	68	1	1	TTC

Figure 1. Mitochondrial map of C. amherstiae and C. pictus.

Table 2. Nucleotide composition in PCGs of mitogenomes of Chrysolophus amherstiae (C.a) and Chrysolophus pictus (C.p).

Gene	A (%)		T (%)		G (%)		C (%)		A + T (%)		G + C (%)
	C.a	C.p	C.a	C.p	C.a	C.p	C.a	C.p	C.a	C.p	C.a	C.p
COX1	26.76	26.5	28.37	28.56	16.44	16.7	28.43	28.24	55.13	55.06	44.87	44.94
COX2	29.24	29.39	26.61	26.46	14.77	14.62	29.39	29.53	55.85	55.85	44.15	44.15
COX3	27.68	27.81	25.77	25.13	15.43	15.43	31.12	31.63	53.44	52.93	46.56	47.07
ND1	27.18	27.18	25.95	26.05	12.62	12.31	34.26	34.46	53.13	53.23	46.87	46.77
ND2	32.44	32.44	25.6	25.6	8.37	8.37	33.59	33.59	58.04	58.04	41.96	41.96
ND3	27.92	28.21	26.21	26.21	12.25	11.97	33.61	33.62	54.13	54.42	45.87	45.58
ND4	31.2	31.13	33.44	23.58	9.8	9.87	35.56	35.41	54.64	54.72	45.36	45.28
ND4L	26.26	25.59	25.25	25.25	12.12	12.79	36.36	36.36	51.52	50.84	48.48	49.16
ND5	31.24	31.3	23.6	23.38	10.62	10.62	34.54	34.71	54.84	54.68	45.16	45.32
ND6	13.79	12.26	42.34	41.19	34.1	35.63	9.77	10.92	56.13	53.45	43.87	46.55
ATP6	28.36	28.22	27.34	27.05	9.5	9.65	34.8	35.09	55.7	55.26	44.3	44.74
ATP8	35.15	35.76	24.24	25.45	6.67	6.06	33.94	32.73	59.39	61.21	40.16	38.79
CYTB	27.91	28.17	25.46	25.2	12.34	12.07	34.3	34.56	53.37	53.37	46.63	46.63

Figure 2. The relative synonymous codon usage (RSCU) in the mitogenomes of C. amherstiae and C. pictus.

Figure 3. Prognostic map of 12S rRNA secondary structures in C. amherstiae and C. pictus. The different bases are shown in red. I–IV represent structural domains.

Figure 4. Prognostic map of 16S rRNA secondary structures in C. amherstiae and C. pictus. The different bases are shown in red. The red arrow represents the inserted base. I–VI represent structural domains.

Figure 5. Maximum-likelihood (ML) phylogenetic tree constructed based on complete mitochondrial genomes from 21 species of 10 genera of Phasianidae. Numbers at the branches indicated the bootstrapping values with 10,000 replications. Filled circle represented a sequence from this study.

Figure 6. Bayesian inference (BI) phylogenetic tree constructed based on complete mitochondrial genomes from 21 species of 10 genera of Phasianidae. Numbers at the branches indicated the bootstrapping values with 10 million generations. Filled circle represented a sequence from this study.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. MW880933.