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

doi:10.11978/2017041

摘要/Abstract

摘要：

冠鲽科(Samaridae)隶属于鲽形目(Pleuronectiformes), 包含冠鲽属(Samaris)、沙鲽属(Samariscus)和斜鲽属(Plagiopsetta)。目前研究表明, 冠鲽(Samaris cristatus)和满月沙鲽(Samariscus latus)的线粒体基因组结构都有重排, 并且两者的基因数量也有差别。为检测斜鲽属鱼类中是否也有不同的特征结构, 我们选用褐斜鲽(Plagiopsetta glossa)作为代表种进行斜鲽属鱼类线粒体基因组特征分析, 同时与冠鲽属及沙鲽属鱼类的线粒体基因组特征进行对比。分析显示, 褐斜鲽的线粒体基因组全长为18723bp, 包括39个基因: 13个蛋白基因、24个tRNA基因、2个rRNA基因、2个控制区、1个轻链复制起点和比典型基因组多的13个间隔子。和经典鱼类的线粒体基因组相比, 褐斜鲽和满月沙鲽都多了tRNA-Cys和tRNA-Tyr两个tRNA, 冠鲽只多了tRNA-Cys, 且3个种类都多了一个控制区, 但褐斜鲽与满月沙鲽的基因排列顺序相同。褐斜鲽线粒体基因的重排导致不同位置的6个tRNA形成了六连体基因簇“tRNA-Cys₁-Tyr₁- Ser1-Lys-Arg-Ser2”, “ND5-ND6-Glu-Cytb-Thr”则位于六连体之后, 但这11个基因相对的排序没有发生变化。采用双复制随机丢失模型(double replications and random loss, DRRL)对褐斜鲽基因的重排现象进行分析, 认为该鱼类基因数量、排列顺序以及比典型基因组多13个间隔子等特征为该模型提供了新的依据。

关键词: 鲽形目, 冠鲽科, 线粒体基因组, 基因重排, 分子进化

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

中图分类号:

P735.541

董江星, 时伟, 孔晓瑜, 陈世喜. 褐斜鲽(Plagiopsetta glossa)线粒体基因组特征及重排机制研究[J]. 热带海洋学报, 2018, 37(1): 1-11.

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.

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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