褐斜鲽(Plagiopsetta glossa)线粒体基因组特征及重排机制研究

doi:10.11978/2017041

Abstract

Abstract:

The family Samaridae in Pleuronectiformes consists of three genera, namely, Plagiopsetta, Samariscus and Samaris. Studies on mitochondrial genomes of Samaris cristatus and Samariscus latus showed that there exist differences in genomic rearrangement and gene number between this two species. To determine whether there are structural differences in the species of the genus Plagiopsetta, Plagiopsetta glossa were used as the representative species for this study, and the mitochondrial genomic characteristics of this species were compared with those of Samariscus and Samaris. The length of its mitogenome is 18,723 bp, and contains 39 genes, including 13 protein-coding genes, two rRNA genes, 24 tRNA genes, two control regions, one light strand replication origin, and 13 more interspaces. Compared with the typical mitogenome in teleosts, P. glossa and S. latus have two more genes of tRNA-Cys and tRNA-Tyr (S. cristatus only one more tRNA-Cys). Additionally, each of the three flatfish has an extra control region, but the gene orders of P. glossa and S. latus mitogenomes are the same. Six genes (tRNA-Cys₁, tRNA-Tyr₁, tRNA-Ser1, tRNA-Lys, tRNA-Arg, and tRNA-Ser2) from different locations are clustered together forming a gene cluster, and following by this genes cluster was ND5-ND6-Glu-Cytb-Thr, all those 11 genes have no gene order change in terms of typical mitogenome.

The model of Double Replications and Random Loss was used to analyze the possible rearrangement mechanism in P. glossa mitogenome. The characteristics of gene number, gene order and 13 more interspaces provided new evidence to support the applicability of this model. The results of this study not only enrich our scientific knowledge of mitogenomic features, but also provide more data for further study on mitochondrial evolution and phylogenetic analysis for flatfish.

Key words: Pleuronectiformes, Samaridae, mitogenome, gene rearrangement, molecular evolution

CLC Number:

P735.541

Jiangxing DONG, Wei SHI, Xiaoyu KONG, Shixi CHEN. Characteristic analysis of the complete mitogenome of Plagiopsetta glossa and a possible mechanism for gene rearrangement[J].Journal of Tropical Oceanography, 2018, 37(1): 1-11.

Figures/Tables 5

Tab. 1

Fig. 1

Tab. 2

Fig. 2

Fig. 3

The inferred mechanism of gene rearrangement from the ancestral gene order to that of P. glossa mitogenome based on the DRRL model. Protein-coding genes and rRNA are indicated by boxes, and tRNA genes are indicated by columns. Genes labeled above the diagram are encoded by the H-strand, and the others, by the L-strand. OH indicates the origin of replication for the H-strand; the direction of replication is shown by arrows. The dark boxes indicate the control regions (CRs), noncoding region (NC) and intergenic spacers. (a) The ancestral mitogenome with 37 genes and one CR. (b) The ancestral CR was duplicated to CRⅠ and CRⅡ, and then CRⅠ was translocated to the position between tRNA-Q and tRNA-M. A first mitochondrial replication event (RP1) was initiated at OHⅠ. (c) After RP1 passed through OHⅡ, secondary replication (RP2) began at OHⅡ. Both replications terminated close to the site of OHⅠ. (d) The duplication of 29 genes and one CR yielded by double replications. (e) One of each copied gene pair was lost randomly. Dark gray boxes indicate degenerated genes. The italic lines indicate the positions of intergenetic spaces from the degenerated genes. The numbers marked by prime indicate the order of the intergenetic spaces in genenome. (f) The order of genes, CRs and intergenic spaces after the loss of several genes. (g) The mitogenome of P. glossa was formed after CRⅠ-tRNA-C1-Y1 and the first 41 bp of Non-coding sequence 1 duplicated and translocated to the position between tRNA-L2 and tRNA-P. (h) The positions and lengths of intergenic spacers of P. glossa. The number in black shaded boxes indicate the intergenic spacer order in mitogenome. The numbers in the boxes above and below represent the length of the intergenic spacers. The boxes above the diagram indicate the sites of intergenic spacers same as the typical one in teleosts; the others are only in P. glossa"

Fig. 3

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正向引物	序列(5′—3′)	反向引物	序列(5′—3′)
Z15	ATTAAAGCATAACHCTGAAGATGTTAAGAT	F2753	TAGATAGAAACTGACCTGGATTACTCCGGT
Z2625	GTTTACGACCTCGATGTTGGATCAGGACAT	F6746	GCGGTGGATTGTAGACCCATARACAGAGGT
Z-Ile	AAGGRHYACTTTGATAGAG	FND5-1180	ATRATNGCRTCYTTDGARWARAANCC
ZND5-1050	GCNATRCTNTTYYTNTGYTCNGGNTC	F-Cytb	TGNCCRATRAKVAYRWADGGRTSTTC
ZND6-210	GCHARNGCNRCHGARTANGCAAA	FCOI-70	CCHACYATNCCDGCYCARGCMCCRAA
Z6468	CCACATCTDCTGCATGCAAAYCAYACACTT	FATP6-495	AGRTGNCCNGCNGTBARRTTNGCNGT
ZATP-310	ACHTTYACNCCHACHACNCARCTNTC	FND4-865	CCYATGTGVCYNACDGADGAGTADGC
Z10818	TTYGAAGCAGCCGCMTGATACTGACAYTT	F13413	TAGCTGCTACTCGGATTTGCACCAAGAGT
Z13347	AAGGATAACAGCTCATCCGTTGGTCTTAGG	F49	GGCCCATCTTAACATCTTC

基因	位置		长度		密码子				间隔区
基因	起始	终止	bp	aa	起始	终止	反密码子	编码链	间隔区
Phe(F)	1	68	68				GAA	H	0
12S	69	1019	951					H	0
Val(V)	1020	1091	72				TAC	H	0
16S	1092	2814	1723					H	0
Leu1(L1)	2815	2888	74				TAA	H	0
ND1	2889	3863	975	324	ATG	TAA		H	0
Ile(I)	3864	3935	72				GAT	H	0
Gln(Q)	3934	4005	72				TTG	L	-2
CR1	4006	4898	893					H	0
Cys₁(C₁)	4899	4966	68				GCA	L	0
Tyr₁(Y₁)	4967	5034	68				GTA	L	0
Ser1(S1)	5176	5246	71				TGA	L	141
Lys(K)	5309	5383	75				TTT	H	62
Arg(R)	5418	5487	70				TCG	H	34
Ser2(S2)	5549	5615	67				GCT	H	61
ND5	5691	7529	1839	612	ATG	TAA		H	75
ND6	7526	8047	522	173	ATG	TAG		L	-4
Glu(E)	8049	8117	69				TTC	L	1
Cytb	8122	9262	1141	380	ATG	T		H	4
Thr(T)	9263	9333	71				TGT	H	0
Met(M)	9341	9409	69				CAT	H	7
ND2	9410	10456	1047	348	ATG	TAG		H	0
Trp(W)	10455	10524	70				TCA	H	-2
Ala(A)	10526	10593	68				TGC	L	1
Asn(N)	10595	10667	73				GTT	L	1
O_L	10663	10706	44					L	-5
COⅠ	10724	12274	1551	516	GTG	TAA		H	17
Asp(D)	12306	12373	68				GTC	H	31
COⅡ	12381	13079	699	232	ATG	AGA		H	7
ATP8	13141	13308	168	55	ATG	TAA		H	61
ATP6	13299	13982	684	227	ATG	TAA		H	-10
COⅢ	13982	14767	786	261	ATG	TAA		H	-1
Gly(G)	14767	14836	70				TCC	H	-1
ND3	14837	15187	351	116	ATG	TAA		H	0
ND4L	15261	15557	297	98	ATG	TAA		H	73
ND4	15551	16924	1374	457	ATG	AGA		H	-7
His(H)	16932	17000	69				GTG	H	7
Leu2(L2)	17028	17100	73				TAG	H	27
CR2	17101	17997	897					H	0
Cys₂(C₂)	17998	18065	68				GCA	L	0
Tyr₂(Y₂)	18066	18133	68				GTA	L	0
Pro(P)	18436	18506	71				TGG	L	302
NC	18507	18723	217					H	0

Characteristic analysis of the complete mitogenome of Plagiopsetta glossa and a possible mechanism for gene rearrangement

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