食蟹豆齿鳗线粒体基因组结构特征及系统进化分析

doi:10.11978/2023196

Abstract

Abstract:

Pisodonophis cancrivorus is an important fish species in the southeast coast of China. In this study, the complete mitochondrial genome of P. cancrivorus was obtained by high-throughput sequencing technique, as well as the structural characteristics and phylogenetic relationships were also analyzed. The total length of the complete mitochondrial DNA is 17650bp, and the base compositions are A (31.72%), G (15.58%), T (26.26%) and C (26.44%), respectively, showing an obvious anti-G bias and A+T preference. Similar to the published mitogenomes of Ophichthidae species, some genes have undergone a tandem duplication-random loss (TDRL) event due to the natural selection, causing the ND6 gene and its conjoint tRNA-Glu(E) to be translocated between tRNA-Thr(T) and tRNA-Pro(P). Besides, another D-loop region with length of 966bp is located upstream of the ND6 gene, and these two D-loop regions show a trend of independent evolution. There are two start codons (ATG, GTG) and four stop codons (TAG, TAA, TA-, T--) among the 13 protein-coding genes (PCGs), and only COI gene is initiated with GTG. In the total of 3 824 encoded amino acids, the content of Leu is the highest, while the content of Cys is the lowest. There are 17 DNA mismatches in the secondary structures of 22 tRNAs. All tRNAs can form the clover-leaf structures, excepting tRNA-Ser^AGY(S) because of lacking the DHU arm. The origin of L-strand replication region (O_L) with the length of 21bp is situated in the “WANCY” region, and the conserved motif 3'-GGCGG-5' is detected in the 3' end of its hairpin secondary structure. The sequences of 12 PCGs (without ND6) are concatenated by removing stop codons, and the interspecific genetic distances of 17 Ophichthidae fishes are calculated to be 0.128-0.297 based on the Kimura two-parameter (K2P) model. The phylogenetic trees constructed by the maximum likelihood (ML) and Bayesian inference (BI) methods show a complex evolutionary relationship of Ophichthidae fishes. P. cancrivorus is located at the base of the phylogenetic tree and closely related to Ophichthus brevicaudatus and O. evermanni, suggesting that it may diverge later than other snake eels.

Key words: Pisodonophis cancrivorus, mitochondrial genome, structure characteristics, sequence analysis, phylogeny

CLC Number:

S917.4

YANG Lan, ZHAO Yao, LIU Yuping, YANG Tianyan. The mitochondrial genomic characteristics and phylogenetic relationship analysis of Pisodonophis cancrivorus (Anguilliformes, Ophichthidae)[J].Journal of Tropical Oceanography, 2024, 43(6): 145-159.

Figures/Tables 10

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基因	编码链	起始位点	终止位点	长度/bp	基因间隔/bp	编码氨基酸数量	起始密码子	终止密码子	反密码子
tRNA-Phe(F)	H	1	68	68	0				GAA
12S rRNA	H	69	1 027	959	0
tRNA-Val(V)	H	1 028	1 098	71	0				TAC
16S rRNA	H	1 099	2 799	1 701	0
tRNA-Leu^UUR(L)	H	2 800	2 875	76	0				TAA
ND1	H	2 876	3 844	969	0	322	ATG	TAA
tRNA-Ile(I)	H	3 847	3 919	73	2				GAT
tRNA-Gln(Q)	L	3 919	3 989	71	-1				TTG
tRNA-Met(M)	H	3 989	4 057	69	-1				CAT
ND2	H	4 058	5 114	1 057	0	352	ATG	T--
tRNA-Trp(W)	H	5 115	5 183	69	0				TCA
tRNA-Ala(A)	L	5 185	5 253	69	1				TGC
tRNA-Asn(N)	L	5 255	5 327	73	1				GTT
O_L	H	5 329	5 349	21	1
tRNA-Cys(C)	L	5 371	5 437	67	21				GCA
tRNA-Tyr(Y)	L	5 438	5 509	72	0				GTA
COI	H	5 511	7 151	1 641	1	546	GTG	TAA
tRNA-Ser^UCN(S)	L	7 169	7 239	71	17				TGA
tRNA-Asp(D)	H	7 245	7 312	68	5				GTC
COII	H	7 319	8 009	691	6	230	ATG	T--
tRNA-Lys(K)	H	8 010	8 084	75	0				TTT
ATP8	H	8 086	8 253	168	1	55	ATG	TAA
ATP6	H	8 244	8 923	680	-10	226	ATG	TA-
COIII	H	8 924	9 708	785	0	261	ATG	TA-
tRNA-Gly(G)	H	9 709	9 780	72	0				TCC
ND3	H	9 781	10 129	349	0	116	ATG	T--
tRNA-Arg(R)	H	10 130	10 199	70	0				TCG
ND4L	H	10 200	10 496	297	0	98	ATG	TAA
ND4	H	10 490	11 870	1 381	-7	610	ATG	T--
tRNA-His(H)	H	11 871	11 939	69	0				GTG
tRNA-Ser^AGY(S)	H	11 940	12 009	70	0				GCT
tRNA-Leu^CUN(L)	H	12 010	12 082	73	0				TAG
ND5	H	12 083	13 918	1 836	0	611	ATG	TAG
Cyt b	H	13 933	15 073	1 141	14	380	ATG	T--
tRNA-Thr(T)	H	15 074	15 145	72	0				TGT
D-loop1	H	15 146	16 111	966	0
ND6	L	16 112	16 630	519	0	172	ATG	TAG
tRNA-Glu(E)	L	16 631	16 699	69	0				TTC
tRNA-Pro(P)	L	16 703	16 775	73	3				TGG
D-loop2	H	16 776	17 650	875	0

基因/区域	长度/bp	A/%	T/%	G/%	C/%	A+T/%	AT偏倚	GC偏倚
线粒体全序列	17 650	31.72	26.26	15.58	26.44	57.98	0.094	-0.259
13个蛋白质编码基因	11 514	29.33	28.23	15.46	26.98	57.56	0.019	-0.271
密码子第1位点	3 849	28.55	23.33	22.79	25.33	51.88	0.101	-0.053
密码子第2位点	3 831	23.52	35.47	13.94	27.07	58.99	-0.203	-0.320
密码子第3位点	3 834	35.92	25.93	9.62	28.53	61.85	0.162	-0.496
ND1	969	27.86	27.86	15.38	28.90	55.72	0.000	-0.305
ND2	1 057	33.59	24.50	13.62	28.29	58.09	0.156	-0.350
COI	1 641	28.28	29.25	17.55	24.92	57.53	-0.017	-0.174
COII	691	30.82	26.19	15.63	27.36	57.01	0.081	-0.273
ATP8	168	33.33	25.00	10.12	31.55	58.33	0.143	-0.514
ATP6	680	29.12	28.97	12.35	29.56	58.09	0.003	-0.411
COIII	785	28.15	27.90	17.20	26.75	56.05	0.004	-0.217
ND3	349	28.37	31.52	14.04	26.07	59.89	-0.053	-0.300
ND4L	297	28.28	26.60	13.47	31.65	54.88	0.031	-0.403
ND4	1 381	29.98	27.59	13.76	28.67	57.57	0.042	-0.351
ND5	1 836	32.57	26.85	12.91	27.67	59.42	0.096	-0.364
Cyt b	1 141	28.66	29.71	15.07	26.56	58.37	-0.018	-0.276
ND6	519	38.73	15.03	14.06	32.18	53.76	0.441	-0.392
12S rRNA	959	33.58	21.38	20.02	25.02	54.96	0.222	-0.111
16S rRNA	1 701	37.92	19.05	18.99	24.04	56.97	0.331	-0.117
D-loop1	966	32.19	32.51	14.29	21.01	64.70	0.441	-0.392
D-loop2	875	36.23	29.60	10.74	23.43	65.83	0.441	-0.392

密码子	计数	RSCU	密码子	计数	RSCU	密码子	计数	RSCU	密码子	计数	RSCU
UUU(F)	121	1.07	UCU(S)	30	0.76	UAU(Y)	62	0.96	UGU(C)	10	0.61
UUC(F)	105	0.93	UCC(S)	63	1.59	UAC(Y)	67	1.04	UGC(C)	23	1.39
UUA(L)	101	1.02	UCA(S)	84	2.12	UAA(*)	0	0.00	UGA(W)	108	1.79
UUG(L)	31	0.31	UCG(S)	4	0.10	UAG(*)	1	0.80	UGG(W)	13	0.21
CUU(L)	108	1.09	CCU(P)	32	0.58	CAU(H)	33	0.67	CGU(R)	11	0.58
CUC(L)	108	1.09	CCC(P)	67	1.22	CAC(H)	66	1.33	CGC(R)	10	0.53
CUA(L)	190	1.92	CCA(P)	107	1.95	CAA(Q)	84	1.75	CGA(R)	46	2.42
CUG(L)	55	0.56	CCG(P)	14	0.25	CAG(Q)	12	0.25	CGG(R)	9	0.47
AUU(I)	202	1.43	ACU(T)	48	0.6	AAU(N)	53	0.73	AGU(S)	13	0.33
AUC(I)	81	0.57	ACC(T)	100	1.25	AAC(N)	92	1.27	AGC(S)	44	1.11
AUA(M)	155	1.52	ACA(T)	159	1.99	AAA(K)	79	1.72	*AGA()**	2	1.60
AUG(M)	49	0.48	ACG(T)	12	0.15	AAG(K)	13	0.28	*AGG()**	2	1.60
GUU(V)	59	1.07	GCU(A)	53	0.68	GAU(D)	25	0.61	GGU(G)	28	0.46
GUC(V)	48	0.87	GCC(A)	129	1.66	GAC(D)	57	1.39	GGC(G)	64	1.06
GUA(V)	89	1.61	GCA(A)	120	1.55	GAA(E)	79	1.65	GGA(G)	118	1.96
GUG(V)	25	0.45	GCG(A)	8	0.10	GAG(E)	17	0.35	GGG(G)	31	0.51

The mitochondrial genomic characteristics and phylogenetic relationship analysis of Pisodonophis cancrivorus (Anguilliformes, Ophichthidae)

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