青海湖裸鲤和花斑裸鲤线粒体基因组比较及其系统进化分析

doi:10.7668/hbnxb.20193633

摘要/Abstract

摘要：

为正确区分青海湖裸鲤和花斑裸鲤,向科学研究及偷捕鱼货物的司法鉴定提供相应的数据支撑。对青海湖裸鲤和花斑裸鲤的线粒体基因组进行测序和生物信息学分析。此外,基于36种鲤科鱼类的线粒体全基因组序列用最大似然法(ML)构建鲤科鱼类系统发育树。结果表明,青海湖裸鲤线粒体基因组全序列全长为16 720 bp,包括13个蛋白编码基因,22个tRNA基因,2个rRNA基因和1个D-Loop控制区,整个青海湖裸鲤线粒体基因组的核苷酸组成为28.68%A、27.29%T、18.16%G及25.87%C,AT偏向性显著(55.97%)。花斑裸鲤线粒体基因组全序列全长为16 760 bp,包括13个蛋白编码基因,22个tRNA基因,2个rRNA基因和1个D-Loop控制区,整个花斑裸鲤线粒体基因组的核苷酸组成为28.63%A、27.22%T、18.26%G及25.88%C,同样具有明显的AT偏向性(55.85%)。青海湖裸鲤和花斑裸鲤线粒体基因组所有蛋白编码基因以ATG作为起始密码子,绝大多数蛋白编码基因以TAG或TAA作为终止密码子,少数以不完全密码子(T--)作为终止密码子,所有的tRNA基因均能形成典型的三叶草结构。系统发育分析结果显示,裸鲤属所有物种都聚为一个类群,并与光倒刺鲃、大理裂腹鱼和扁吻鱼的亲缘关系较近。该研究基于线粒体基因组的系统发育分析未将青海湖裸鲤和花斑裸鲤准确区分,但为重新建立更清晰的鲤科鱼类分类体系奠定了基础。

关键词: 青海湖裸鲤, 花斑裸鲤, 线粒体基因组, 系统发育分析

Abstract:

The study aims to correctly distinguish between Gymnocypris przewalskii and Gymnocypris eckloni,and to provide corresponding data support to scientific research and judicial identification of fish poaching cargo. The mitochondrial genomes of Gymnocypris przewalskii and Gymnocypris eckloni were sequenced and bioinformatics analyzed. In addition,a cyprinid phylogenetic tree was constructed using the maximum likelihood (ML) method based on the complete mitochondrial genome sequences of 36 cyprinid species. The results showed that the total length of the mitochondrial genome of Gymnocypris przewalskii was 16 720 bp,including 13 protein-coding genes,22 tRNA genes,2 rRNA genes and 1 D-Loop control region. The nucleotide composition of the entire mitochondrial genome was A (28.68%),T (27.29%),G (18.16%) and C (25.87%),with a significant AT-bias (55.97%). The total sequence of the mitochondrial genome of Gymnocypris eckloni was 16 760 bp,including 13 protein-coding genes,22 tRNA genes,2 rRNA genes and 1 D-Loop control region. The nucleotide composition of whole mitochondrial genome was A (28.63%),T (27.22%),G (18.26%) and C (25.88%). There was also a significant AT bias (55.85%). All protein-coding genes in the mitochondrial genome of Gymnocypris przewalskii and Gymnocypris eckloni took ATG as the initiation codon,the vast majority of protein-coding genes took TAG or TAA as the termination codon,and a few took incomplete codons (T--) as the termination codon. All tRNA genes could form a typical clover structure. Phylogenetic analysis showed that all species of the genus Gymnocypris were clustered together and were closely related to the Spinibarbus hollandi,Schizothorax taliensis and Aspiorhynchus laticeps. The mitochondrial genome-based phylogenetic analysis of this experimental study did not accurately distinguish the Gymnocypris przewalskii and Gymnocypris eckloni,but laid the foundation for re-establishing a clearer taxonomic system for Cyprinidae.

Key words: Gymnocypris przewalskii, Gymnocypris eckloni, Mitochondrial genome, Phylogenetic analysis

保长虹, 李昭楠, 关却多杰, 李长忠, 尹格玛, 贺彩霞, 金文杰, 周叶吉, 陈艳霞. 青海湖裸鲤和花斑裸鲤线粒体基因组比较及其系统进化分析[J]. 华北农学报, 2023, 38(3): 213-226. doi: 10.7668/hbnxb.20193633.

BAO Changhong, LI Zhaonan, GUANQUE Duojie, LI Changzhong, YIN Gema, HE Caixia, JIN Wenjie, ZHOU Yeji, CHEN Yanxia. Comparison and Phylogenetic Analysis of Mitochondrial Genomes Between Gymnocypris przewalskii and Gymnocypris eckloni[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(3): 213-226. doi: 10.7668/hbnxb.20193633.

http://www.hbnxb.net/CN/Y2023/V38/I3/213

图/表 11

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青海湖裸鲤 Gymnocypris przewalskii	碱基对/bp Base pair	A/%	T/%	G/%	C/%	A+T/%	G+C/%	AT偏倚 AT-skew	GC偏倚 GC-skew
线粒体基因组	16 720	28.68	27.29	18.16	25.87	55.97	44.03	0.025	-0.175
Mitochondrial genome
蛋白编码基因PCGs	11 410	26.45	29.96	17.54	26.05	56.42	43.58	-0.062	-0.195
转运RNA tRNAs	1 562	28.23	26.57	23.82	21.38	54.80	45.20	0.030	0.054
核糖体RNA rRNAs	2 592	33.02	20.72	22.34	23.92	53.74	46.26	0.229	-0.034
mtDNA控制区D-Loop	939	31.74	32.06	14.80	21.41	63.79	36.21	-0.005	-0.182

青海湖裸鲤 Gymnocypris przewalskii	碱基对/bp Base pair	A/%	T/%	G/%	C/%	A+T/%	G+C/%	AT偏倚 AT-skew	GC偏倚 GC-skew
线粒体基因组	16 720	28.68	27.29	18.16	25.87	55.97	44.03	0.025	-0.175
Mitochondrial genome
蛋白编码基因PCGs	11 410	26.45	29.96	17.54	26.05	56.42	43.58	-0.062	-0.195
转运RNA tRNAs	1 562	28.23	26.57	23.82	21.38	54.80	45.20	0.030	0.054
核糖体RNA rRNAs	2 592	33.02	20.72	22.34	23.92	53.74	46.26	0.229	-0.034
mtDNA控制区D-Loop	939	31.74	32.06	14.80	21.41	63.79	36.21	-0.005	-0.182

花斑裸鲤 Gymnocypris eckloni	碱基对/bp Base pair	A/%	T/%	G/%	C/%	A+T/%	G+C/%	AT偏倚 AT-skew	GC偏倚 GC-skew
线粒体基因组	16 760	28.63	27.22	18.26	25.88	55.85	44.15	0.025	-0.173
Mitochondrial genome
蛋白编码基因PCGs	11 410	26.45	29.96	17.54	26.06	56.41	43.59	-0.062	-0.195
转运RNA tRNAs	1 562	28.10	26.57	23.94	21.38	54.67	45.33	0.028	0.056
核糖体RNA rRNAs	2 592	32.99	20.68	22.38	23.96	53.67	46.33	0.229	-0.034
mtDNA控制区D-Loop	939	31.84	32.06	14.70	21.41	63.90	36.10	-0.003	-0.186

花斑裸鲤 Gymnocypris eckloni	碱基对/bp Base pair	A/%	T/%	G/%	C/%	A+T/%	G+C/%	AT偏倚 AT-skew	GC偏倚 GC-skew
线粒体基因组	16 760	28.63	27.22	18.26	25.88	55.85	44.15	0.025	-0.173
Mitochondrial genome
蛋白编码基因PCGs	11 410	26.45	29.96	17.54	26.06	56.41	43.59	-0.062	-0.195
转运RNA tRNAs	1 562	28.10	26.57	23.94	21.38	54.67	45.33	0.028	0.056
核糖体RNA rRNAs	2 592	32.99	20.68	22.38	23.96	53.67	46.33	0.229	-0.034
mtDNA控制区D-Loop	939	31.84	32.06	14.70	21.41	63.90	36.10	-0.003	-0.186

基因名称 Gene	定位 Direction	起始~终止位置/bp Start-Stop location	序列长度 /bp Size	反密码子 (定位区间) Anticodon (location interval)	起始密码子 Start codon	终止密码子 Stop codon	基因间隔核苷酸区 Intergenic nucleotides
trnF	+	1~69	69	32~34(GAA)			0
rrnS	+	70~1 026	957				0
trnV	+	1 029~1 100	72	1 062~1 064(TAC)			2
rrnL	+	1 123~2 757	1 635				22
trnL2	+	2 782~2 857	76	2 818~2 820(TAA)			24
nad1	+	2 859~3 833	975		ATG	TAG	1
trnI	+	3 837~3 908	72	3 869~3 871(GAT)			3
trnQ	-	3 907~3 977	71	3 943~3 945(TTG)			-2
trnM	+	3 980~4 048	69	4 010~4 012(CAT)			2
nad2	+	4 049~5 093	1 045		ATG	T--	0
trnW	+	5 094~5 164	71	5 126~5 128(TCA)			0
trnA	-	5 166~5 234	69	5 202~5 204(TGC)			1
trnN	-	5 236~5 308	73	5 273~5 275(GTT)			1
trnC	-	5 342~5 407	66	5 378~5 380(GCA)			33
trnY	-	5 407~5 477	71	5 443~5 445(GTA)			-1
cox1	+	5 479~7 029	1 551		GTG	TAA	1
trnS2	-	7 030~7 100	71	7 066~7 068(TGA)			0
trnD	+	7 104~7 175	72	7 137~7 139(GTC)			3
cox2	+	7 189~7 879	691		ATG	T--	13
trnK	+	7 880~7 955	76	7 916~7 918(TTT)			0
atp8	+	7 957~8 121	165		ATG	TAG	1
atp6	+	8 115~8 798	684		ATG	TAA	-7
cox3	+	8 798~9 582	785		ATG	TA-	-1
trnG	+	9 583~9 654	72	9 616~9 618(TCC)			0
nad3	+	9 655~10 003	349		ATG	T--	0
trnR	+	10 004~10 073	70	10 035~10 037(TCG)			0
nad4l	+	10 074~10 370	297		ATG	TAA	0
nad4	+	10 364~11 744	1 381		ATG	T--	-7
trnH	+	11 745~11 813	69	11 775~11 777(GTG)			0
trnS1	+	11 814~11 882	69	11 841~11 843(GCT)			0
trnL1	+	11 884~11 956	73	11 917~11 919(TAG)			1
nad5	+	11 960~13 783	1 824		ATG	TAA	3
nad6	-	13 780~14 301	522		ATG	TAA	-4
trnE	-	14 302~14 370	69	14 338~14 340(TTC)			0
cob	+	14 375~15 515	1 141		ATG	T--	4
trnT	+	15 516~15 587	72	15 548~15 550(TGT)			0
trnP	-	15 712~15 781	70	15 748~15 750(TGG)			124
D-Loop	+	15 782~16 720	939				0

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