基于Illumina Hiseq 4000 高通量测序平台的暗色唇鲮线粒体基因组特征分析

韩耀全; 黄励; 朱琼华; 吴伟军; 何安尤; 施军; 李育森

doi:10.19303/j.issn.1008-0384.2020.02.003

基于Illumina Hiseq 4000 高通量测序平台的暗色唇鲮线粒体基因组特征分析

doi: 10.19303/j.issn.1008-0384.2020.02.003

1.
广西水产遗传育种与健康养殖重点实验室/广西水产科学研究院，广西　南宁　530021
2.
广西国际商务职业技术学院，广西　南宁　530007
3.
广州瑞科基因科技有限公司，广东　广州　510540

基金项目: 广西自然科学基金重大专项（2013GXNSFEA053003）；广西水产遗传育种与健康养殖重点实验室建设项目（17-259-29）

详细信息

作者简介:
韩耀全（1969−），男，高级工程师，主要从事水生生物自然资源及水生生态调查、保护与修复工作（E-mail：hyqao@sohu.com）

中图分类号: Q 173；Q 959.46+8
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出版历程
- 收稿日期: 2019-11-15
- 修回日期: 2020-01-07
- 刊出日期: 2020-02-01

Characteristics of Mitochondrial Genomes of Semilabeo obscures Analyzed Using Illumina Hiseq 4000 High-throughput Sequencing Technique

1.
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture/Guangxi Academy of Fishery Sciences, Nanning, Guangxi　530021, China
2.
Guangxi International Business Vocational College, Nanning, Guangxi　530007, China
3.
Science Corporation of Gene, Guangzhou, Guangdong　510540, China

摘要

摘要: 目的研究暗色唇鲮（Semilabeo obscurus）的分子遗传学特性，为暗色唇鲮种质资源遗传多样性分析和分子标记研究提供基础数据。方法利用高通量第二代测序技术，构建暗色唇鲮线粒体基因组全序列，分析序列的结构特征。结果暗色唇鲮的线粒体基因组全序列长度16 598～16 599 bp，GC含量42.65%～42.7%，共含有13个蛋白编码基因、22个tRNA、2个rRNA（12S-rRNA和16S-rRNA）以及1个控制区。线粒体基因组除ND6外，GC-skew值均为负值，COXI、ND3以及ND6的AT-skew值为负值，其余基因的AT-skew值均为正值。暗色唇鲮的13个蛋白编码基因氨基酸总长为3 794 aa，偏好密码子（RSCU＞2）分别是终止密码子Arg（CGA）、Gly（GGA）、Leu（CTA）、Pro（CCA）、Ser（TCA）以及终止密码子Stp（TAA）。暗色唇鲮（唇鲮属Semilabeo）与泉水鱼Pseudogyrinocheilus prochilus的亲缘关系最近，和卷口鱼Ptychidio jordani、直口鲮Rectoris posehensis、异华鲮Parasinilabeo assimilis存在较高的亲缘关系。结论暗色唇鲮的线粒体基因组结构和基因排列顺序与鱼类基因组典型结构和排列一致。
- 暗色唇鲮 /
- 线粒体基因组 /
- 结构特征 /
- 系统发育
Abstract: Objective Molecular genetics of various Dusky Labiaet-barbel (Semilabeo obscures) was studied. Method The second-generation Illumina Hiseq 4000 high-throughput sequencing technology was employed to determine the sequences of the mitochondrial genomes of different species of S. obscures. Result The length of the individual mitochondrial genome was determined to be 16 598–16 599 bp containing 42.65%–42.7% GC. There were 13 protein-coding genes, 22 tRNA, 2 rRNA (i.e., 12S-rRNA and 16S-rRNA), and one control region. Except for the coded ND6, the values of GC-skew of the genomes were all negative; while those of AT-skew in COXI, ND3 and ND6 were negative as well; but those of AT-skew in others were positive. The 13 protein-coding genes consisted of 3 794 aa with the preference codon (RSCU＞2) including the termination codon Arg (CGA), Gly (GGA), Leu (CTA), Pro (CCA), Ser (TCA) and the termination codon Stp (TAA). These S. obscures appeared to relate most closely with Pseudogyrinocheilus prochilus and somewhat with Ptychidio jordani, Rectoris posehensis and Parasinilabeo assimilis. Conclusion The structures and sequences of the mitochondrial genomes of S. obscures as determined were in line with those of typical fish counterparts.
- Semilabeo obscures /
- mitochondrial genome /
- structure and characteristics /
- phylogeny

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图 1 暗色唇鲮线粒体基因组结构和排列

Figure 1. Structures and sequences of mitochondrial genomes of S. obscures

下载: 全尺寸图片幻灯片

图 2 暗色唇鲮线粒体基因组密码子使用频率分布

Figure 2. Frequency distribution of codon usage in mitochondrial genomes of S. obscures

下载: 全尺寸图片幻灯片

图 3 暗色唇鲮的系统发育进化树

Figure 3. Phylogenetic trees based on nucleotides of S. obscures

下载: 全尺寸图片幻灯片

表 1 暗色唇鲮的线粒体基因组特征

Table 1. Characteristics of mitochondrial genomes of S. obscures

基因/区域 Gene /Area	因子 Factor	云南暗色唇鲮 YN	贵州暗色唇鲮 GZ	广西暗色唇鲮 GX
全基因组 Whole genome	序列长度 Length/bp	16 598	16 598	16 599
	A和T碱基之和所占比例 AT Ratio/%	57.30	57.33	57.35
	AT偏移率 AT-skew	0.113 4	0.112 4	0.112 8
	GC偏移率 GC-skew	−0.265 1	−0.264 3	−0.264 6
蛋白质编码基因 Protein-coding genes	序列长度 Length（aa）	3 794	3 794	3 794
	A和T碱基之和所占比例（总） AT Ratio /%（all）	57.37	57.41	57.44
	每隔2个碱基取第3个碱基组成的新序列的A和T碱基之和所占比例 AT Ratio/%（3rd）	58.98	59.00	59.00
	AT偏移率 AT-skew	0.084 4	0.082 6	0.082 8
	GC偏移率 GC-skew	−0.332 1	−0.330 3	−0.330 6
16S核糖体核糖核酸 rrnL	序列长度 Length/bp	1 686	1 686	1 686
	A和T碱基之和所占比例 AT Ratio/%	56.58	56.58	56.70
	AT偏移率 AT-skew	0.314 5	0.314 5	0.313 8
	GC偏移率 GC-skew	−0.090 2	−0.090 2	−0.090 4
12S核糖体核糖核酸 rrnS	序列长度 Length/bp	956	956	956
	A和T碱基之和所占比例 AT Ratio/%	51.78	51.67	51.67
	AT偏移率 AT-skew	0.256 6	0.255 1	0.255 1
	GC偏移率 GC-skew	−0.102	−0.099 6	−0.099 6
转运核糖核酸 tRNAs	序列长度 Length/bp	1 562	1 562	1 562
	A和T碱基之和所占比例 AT Ratio/%	55.70	55.70	55.57
	AT偏移率 AT-skew	0.110 3	0.112 6	0.110 6
	GC偏移率 GC-skew	−0.112 7	−0.115 6	−0.112 4
控制区 Control area	序列长度 Length/bp	937	937	937
	A和T碱基之和所占比例 AT Ratio/%	66.7	66.92	66.81
	AT偏移率 AT-skew	0.004 8	0.008 0	0.016 0
	GC偏移率 GC-skew	−0.211 5	−0.219 4	−0.228 3

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表 2 暗色唇鲮线粒体基因组注释结果（云南）

Table 2. Complete annotation of mitochondrial genome of S. obscures (YN)

基因 Gene	编码链 Coding strand	起始位点 Start position	终止位点 Stop position	长度 Size/bp	GC含量 G+C content/%	氨基酸 aa	起始密码子 Start codons	终止密码子 Stop codons	反密码子 Anticodon	间隔碱基 Intergenic nucleotide/bp
tRNA-Phe	H	1	69	69	43.48%				GAA	0
12S-rRNA	H	70	1 025	956	48.22%					0
tRNA-Val	H	1 026	1 097	72	51.39%				TAC	0
16S-rRNA	H	1 098	2 783	1 686	43.42%					0
tRNA-Leu	H	2 784	2 859	76	52.63%				TAA	1
ND1	H	2 861	3 835	975	44.31%	324	ATG	TAA		4
tRNA-Ile	H	3 840	3 911	72	47.22%				GAT	−2
tRNA-Gln	L	3 910	3 980	71	42.25%				TTG	1
tRNA-Met	H	3 982	4 050	69	57.97%				CAT	0
ND2	H	4 051	5 097	1 047	44.13%	348	ATG	TAG		−2
tRNA-Trp	H	5 096	5 166	71	38.03%				TCA	2
tRNA-Ala	L	5 169	5 237	69	30.43%				TGC	1
tRNA-Asn	L	5 239	5 311	73	47.95%				GTT	33
tRNA-Cys	L	5 345	5 410	66	46.97%				GCA	1
tRNA-Tyr	L	5 412	5 482	71	59.15%				GTA	1
COXI	H	5 484	7 034	1 551	43.39%	516	GTG	TAA		0
tRNA-Ser	L	7 035	7 105	71	49.30%				TGA	3
tRNA-Asp	H	7 109	7 180	72	36.11%				GTC	13
COXII	H	7 194	7 884	691	42.98%	230	ATG	T		0
tRNA-Lys	H	7 885	7 960	76	46.05%				TTT	1
ATP8	H	7 962	8 126	165	39.39%	54	ATG	TAA		−7
ATP6	H	8 120	8 803	684	40.64%	227	ATG	TAA		−1
COXIII	H	8 803	9 588	786	44.40%	261	ATG	TAA		−1
tRNA-Gly	H	9 588	9 659	72	34.72%				TCC	0
ND3	H	9 660	10 010	351	44.16%	116	ATG	TAG		−2
tRNA-Arg	H	10 009	10 078	70	47.14%				TCG	0
ND4L	H	10 079	10 375	297	45.79%	98	ATG	TAA		−7
ND4	H	10 369	11 749	1 381	41.42%	460	ATG	T		0
tRNA-His	H	11 750	11 818	69	30.43%				GTG	0
tRNA-Ser	H	11 819	11 887	69	36.23%				GCT	1
tRNA-Leu	H	11 889	11 961	73	43.84%				TAG	3
ND5	H	11 965	13 788	1 824	40.90%	607	ATG	TAA		−4
ND6	L	13 785	14 306	522	44.83%	173	ATG	TAG		0
tRNA-Glu	L	14 307	14 375	69	39.13%				TTC	4
Cytb	H	14 380	15 520	1 141	40.93%	380	ATG	T		0
tRNA-Thr	H	15 521	15 592	72	51.39%				TGT	−1
tRNA-Pro	L	15 592	15 661	70	41.43%				TGG	0
D-loop	H	15 662	16 598	937	33.30%					0

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表 3 暗色唇鲮线粒体基因组注释结果（贵州）

Table 3. Complete annotation of mitochondrial genome of S. obscures (GZ)

基因 Gene	编码链 Coding strand	起始位点 Start position	终止位点 Stop position	长度 Size/bp	GC含量 G+C content/%	氨基酸 aa	起始密码子 Start codons	终止密码子 Stop codons	反密码子 Anticodon	间隔碱基 Intergenic nucleotide/bp
tRNA-Phe	H	1	69	69	43.48%				GAA	0
12S-rRNA	H	70	1 025	956	48.33%					0
tRNA-Val	H	1 026	1 097	72	50.00%				TAC	0
16S-rRNA	H	1 098	2 783	1 686	43.42%					0
tRNA-Leu	H	2 784	2 859	76	52.63%				TAA	1
ND1	H	2 861	3 835	975	44.41%	324	ATG	TAA		4
tRNA-Ile	H	3 840	3 911	72	47.22%				GAT	−2
tRNA-Gln	L	3 910	3 980	71	42.25%				TTG	1
tRNA-Met	H	3 982	4 050	69	57.97%				CAT	0
ND2	H	4 051	5 097	1 047	44.13%	348	ATG	TAG		−2
tRNA-Trp	H	5 096	5 166	71	38.03%				TCA	2
tRNA-Ala	L	5 169	5 237	69	30.43%				TGC	1
tRNA-Asn	L	5 239	5 311	73	47.95%				GTT	33
tRNA-Cys	L	5 345	5 410	66	46.97%				GCA	1
tRNA-Tyr	L	5 412	5 482	71	59.15%				GTA	1
COXI	H	5 484	7 034	1 551	43.46%	516	GTG	TAA		0
tRNA-Ser	L	7 035	7 105	71	49.30%				TGA	3
tRNA-Asp	H	7 109	7 180	72	36.11%				GTC	13
COXII	H	7 194	7 884	691	42.98%	230	ATG	T		0
tRNA-Lys	H	7 885	7 960	76	46.05%				TTT	1
ATP8	H	7 962	8 126	165	38.79%	54	ATG	TAA		−7
ATP6	H	8 120	8 803	684	40.35%	227	ATG	TAA		−1
COXIII	H	8 803	9 588	786	44.40%	261	ATG	TAA		−1
tRNA-Gly	H	9 588	9 659	72	36.11%				TCC	0
ND3	H	9 660	10 010	351	43.87%	116	ATG	TAG		−2
tRNA-Arg	H	10 009	10 078	70	47.14%				TCG	0
ND4L	H	10 079	10 375	297	45.79%	98	ATG	TAA		−7
ND4	H	10 369	11 749	1 381	41.49%	460	ATG	T		0
tRNA-His	H	11 750	11 818	69	30.43%				GTG	0
tRNA-Ser	H	11 819	11 887	69	36.23%				GCT	1
tRNA-Leu	H	11 889	11 961	73	43.84%				TAG	3
ND5	H	11 965	13 788	1 824	40.73%	607	ATG	TAA		−4
ND6	L	13 785	14 306	522	45.02%	173	ATG	TAG		0
tRNA-Glu	L	14 307	14 375	69	39.13%				TTC	4
Cytb	H	14 380	15 520	1 141	40.84%	380	ATG	T		0
tRNA-Thr	H	15 521	15 592	72	51.39%				TGT	−1
tRNA-Pro	L	15 592	15 661	70	41.43%				TGG	0
D-loop	H	15 662	16 598	937	33.08%					0

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表 4 暗色唇鲮线粒体基因组注释结果（广西）

Table 4. Complete annotation of mitochondrial genome of S. obscures (GX)

基因 Gene	编码链 Coding strand	起始位点 Start position	终止位点 Stop position	长度 Size/bp	GC含量 G+C content/%	氨基酸 aa	起始密码子 Start codons	终止密码子 Stop codons	反密码子 Anticodon	间隔碱基 Intergenic nucleotide/bp
tRNA-Phe	H	1	69	69	44.93%				GAA	0
12S-rRNA	H	70	1 025	956	48.33%					0
tRNA-Val	H	1 026	1 097	72	51.39%				TAC	0
16S-rRNA	H	1 098	2 783	1 686	43.30%					0
tRNA-Leu	H	2 784	2 859	76	52.63%				TAA	1
ND1	H	2 861	3 835	975	44.41%	324	ATG	TAA		4
tRNA-Ile	H	3 840	3 911	72	47.22%				GAT	−2
tRNA-Gln	L	3 910	3 980	71	42.25%				TTG	1
tRNA-Met	H	3 982	4 050	69	57.97%				CAT	0
ND2	H	4 051	5 097	1 047	44.13%	348	ATG	TAG		−2
tRNA-Trp	H	5 096	5 166	71	38.03%				TCA	2
tRNA-Ala	L	5 169	5 237	69	30.43%				TGC	1
tRNA-Asn	L	5 239	5 311	73	47.95%				GTT	34
tRNA-Cys	L	5 346	5 411	66	46.97%				GCA	1
tRNA-Tyr	L	5 413	5 483	71	59.15%				GTA	1
COXI	H	5 485	7 035	1 551	43.39%	516	GTG	TAA		0
tRNA-Ser	L	7 036	7 106	71	49.30%				TGA	3
tRNA-Asp	H	7 110	7 181	72	36.11%				GTC	13
COXII	H	7 195	7 885	691	42.84%	230	ATG	T		0
tRNA-Lys	H	7 886	7 961	76	46.05%				TTT	1
ATP8	H	7 963	8 127	165	38.79%	54	ATG	TAA		−7
ATP6	H	8 121	8 804	684	40.20%	227	ATG	TAA		−1
COXIII	H	8 804	9 589	786	44.53%	261	ATG	TAA		−1
tRNA-Gly	H	9 589	9 660	72	36.11%				TCC	0
ND3	H	9 661	10 011	351	44.16%	116	ATG	TAG		−2
tRNA-Arg	H	10 010	10 079	70	47.14%				TCG	0
ND4L	H	10 080	10 376	297	45.45%	98	ATG	TAA		−7
ND4	H	10 370	11 750	1 381	41.20%	460	ATG	T		0
tRNA-His	H	11 751	11 819	69	30.43%				GTG	0
tRNA-Ser	H	11 820	11 888	69	36.23%				GCT	1
tRNA-Leu	H	11 890	11 962	73	43.84%				TAG	3
ND5	H	11 966	13 789	1 824	40.79%	607	ATG	TAA		−4
ND6	L	13 786	14 307	522	44.83%	173	ATG	TAG		0
tRNA-Glu	L	14 308	14 376	69	39.13%				TTC	4
Cytb	H	14 381	15 521	1 141	41.02%	380	ATG	T		0
tRNA-Thr	H	15 522	15 593	72	51.39%				TGT	−1
tRNA-Pro	L	15 593	15 662	70	41.43%				TGG	0
D-loop	H	15 663	16 599	937	33.19%					0

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表 5 偏好密码子RSCU值

Table 5. RSCUs for preference codons in 3 species of S. obscures

氨基酸 Amino acid	密码子 Codon	云南暗色唇鲮 YN		贵州暗色唇鲮 GZ		广西暗色唇鲮 GX
氨基酸 Amino acid	密码子 Codon	数量 Number	使用频率 RSCU	数量 Number	使用频率 RSCU	数量 Number	使用频率 RSCU
Arg	CGA	52	2.737	51	2.684	52	2.737
Gly	GGA	126	2.049	125	2.033	125	2.033
Leu	CTA	248	2.400	249	2.414	249	2.414
Pro	CCA	121	2.283	120	2.264	119	2.256
Ser	TCA	82	2.103	83	2.128	83	2.119
Stp	TAA	7	2.800	7	2.800	7	2.800

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