山东图兰扇头蜱线粒体基因组全序列测定与分析

doi:10.12140/j.issn.1000-7423.2025.03.012

中国寄生虫学与寄生虫病杂志 ›› 2025, Vol. 43 ›› Issue (3): 377-384.doi: 10.12140/j.issn.1000-7423.2025.03.012

山东图兰扇头蜱线粒体基因组全序列测定与分析

于莲琪¹^,²()(), 苏杭丽¹^,², 王爽³, 王志涛⁴, 卜灿灿¹, 吕文祥¹, 王新梅¹^,², 刘丽娟¹^,², 盛兆安³^,^*()(), 张本光¹^,²^,^*()()

1 山东第一医科大学（山东省医学科学院），山东省寄生虫病防治研究所，山东济宁 272033
2 山东第一医科大学（山东省医学科学院）公共卫生与健康管理学院，山东济南 250117
3 济宁医学院基础医学院病原生物学教研室，山东济宁 272067
4 山东第一医科大学（山东省医学科学院）生物医学科学学院（省医药生物技术研究中心），山东济南 250117

收稿日期:2025-01-22 修回日期:2025-03-18 出版日期:2025-06-30 发布日期:2025-06-09
通讯作者: *张本光（ORCID：0000-0002-9522-4757），男，硕士，研究员，从事寄生虫病分子生物学与防控研究。E-mail：benguangzhang@163.com;盛兆安（ORCID：0000-0002-6309-3203），男，博士，讲师，从事寄生虫病分子生物学与防控研究。E-mail：sza9135@163.com
作者简介:于莲琪（ORCID：0009-0009-6317-1521），女，硕士研究生，从事寄生虫病分子生物学与防控研究。E-mail：13009789089@163.com
基金资助:
国家自然科学基金(81902096);济宁医学院贺林院士新医学临床转化工作站科研基金(JYHL2021MS22)

Sequencing and analysis of the complete mitochondrial genome of Rhipicephalus turanicus in Shandong Province

YU Lianqi¹^,²()(), SU Hangli¹^,², WANG Shuang³, WANG Zhitao⁴, BU Cancan¹, LV Wenxiang¹, WANG Xinmei¹^,², LIU Lijuan¹^,², SHENG Zhaoan³^,^*()(), ZHANG Benguang¹^,²^,^*()()

1 Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong Institute of Parasitic Diseases, Jining 272033, Shandong, China
2 School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
3 Department of Pathogenic Biology, School of Basic Medical Sciences, Jining Medical College, Jining 272067, Shandong, China
4 School of Biomedical Sciences (Provincial Pharmaceutical Biotechnology Research Centre), Shandong First Medical University (Shandong Provincial Academy of Medical Sciences), Jinan 250117, Shandong, China

Received:2025-01-22 Revised:2025-03-18 Online:2025-06-30 Published:2025-06-09
Contact: *E-mail: benguangzhang@163.com; sza9135@163.com
Supported by:
National Natural Scienee Foundation of China(81902096);Jining Medical College He Lin Academician New Medicine Clinical Translation Workstation Research Fund(JYHL2021MS22)

摘要/Abstract

摘要：

目的解析图兰扇头蜱（Rhipicephalus turanicus）线粒体全基因组的结构特征与系统发育关系，揭示不同地理种群之间的遗传分化，为进一步开展物种鉴定和系统发育分析等研究提供数据支撑。方法 2023年8月，于山东省济宁市微山县马坡镇的一只家犬体表采集并鉴定图兰扇头蜱雄蜱1只，提取基因组DNA，采用Illumina测序平台二代测序技术进行测序，并利用Novoplasty软件进行序列组装，拼接完整的线粒体基因组全序列，使用MITOS软件对线粒体基因组进行初步功能注释。基于13个蛋白质编码基因（protein-coding gene，PCG）序列，应用最大似然法构建系统进化树。结果测序结果显示，图兰扇头蜱线粒体基因组全长为14 718 bp（GenBank登录号：PV416795），由13个PCG、22个转运RNA基因、2个核糖体RNA和2个非编码区（NCR）组成。线粒体基因组基因之间存在重叠或基因间隔区，碱基组成呈现明显A + T偏向性。PCG以ATA、ATC、ATG和ATT等4种典型的ATN序列作为起始密码子，TAA、TAG、TA、T为终止密码子。在22个tRNA基因二级结构中，除trnC、trnF、trnS1缺少二氢尿嘧啶臂（DHU臂）和二氢尿嘧啶环（DHU环）导致不能形成完整的三叶草结构外，其余均能形成典型的三叶草结构。系统进化分析表明，本研究采集的山东图兰扇头蜱与北京种群（登录号：OM368330）、新疆种群（登录号：KY996841、NC035946、OM368326）共同聚为一支，并与来自以色列（登录号：OQ184023）和沙特阿拉伯（登录号：PP919886）的种群共同构成一个强支持的单系分支。不同地理种群图兰扇头蜱聚为同一高度支持的系统发育分支，表明其具有较强的遗传保守性，同时也显示出一定的地域性遗传分化趋势。结论本研究获得了山东图兰扇头蜱线粒体基因组全序列，符合硬蜱科线粒体基因组特征，不同地理种群间存在潜在的遗传分化趋势。

关键词: 图兰扇头蜱, 线粒体基因组, 系统进化分析

Abstract:

Objective To decipher the mitochondrial genome structure and phylogenetic relationships of Rhipicephalus turanicus and investigate the genetic differentiation among different geographical populations of R. turanicus, so as to provide data supports to species identification and phylogenetic analysis. Methods A male R. turanicus tick was collected and identified from the body surface of a domestic dog in Mapo Township, Weishan County, Jining City, Shandong Province on August 2023, and genomic DNA was extracted from the tick for second-generation sequencing on an Illumina high-throughput platform. The complete mitochondrial genome of R. turanicus was assembled using Novoplasty software and the functions of the complete mitochondrial genome were preliminarily annotated with the MITOS software. In addition, phylogenetic trees were constructed using the maximum likelihood method based on the sequences of 13 protein-coding genes (PCGs). Results Second-generation sequencing showed that the complete mitochondrial genome of R. turanicus was 14 718 bp in length (GenBank accession No.: PV416795), which was consisted of 13 PCGs, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 non-coding regions (NCRs). The complete mitochondrial genome contained overlapping regions or intergenic regions, and the base composition exhibited a clear A + T preference. The PCGs initiated with four typical start codons ATN (ATA, ATC, ATG, and ATT), and terminated with stop codons TAA, TAG, TA and T. Among the secondary structures of 22 tRNA gene, all formed a typical cloverleaf structure except for trnC, trnF, and trnS1, which lacked the dihydrouracil (DHU) arm and DHU loop, resulting in failure in formation of a complete cloverleaf structure. Phylogenetic analysis revealed that the R. turanicus sampled from Shandong Province in this study was clustered with tick populations from Beijing (GenBank accession No.: OM368330) and Xinjiang (GenBank accession No.: KY996841, NC035946, OM368326) into the same clade branch, and was grouped into a strongly supported monophyletic clade with populations from Israel (GenBank accession No.: OQ184023) and Saudi Arabia (GenBank accession No.: PP919886). The R. turanicus populations from different geographic regions were clustered into a highly supported phylogenetic clade, suggesting a high degree of genetic conservation and a tendency towards regional genetic differentiation. Conclusion The complete mitochondrial genome sequence of R. turanicus from Shandong Province has been obtained, which conforms to the mitochondrial genome characteristics of the Ixodidae family, and there is a tendency towards potential genetic differentiation among different geographic populations of R. turanicus.

Key words: Rhipicephalus turanicus, Mitochondrial genome, Phylogenetic analysis

中图分类号:

R384.41

于莲琪, 苏杭丽, 王爽, 王志涛, 卜灿灿, 吕文祥, 王新梅, 刘丽娟, 盛兆安, 张本光. 山东图兰扇头蜱线粒体基因组全序列测定与分析[J]. 中国寄生虫学与寄生虫病杂志, 2025, 43(3): 377-384.

YU Lianqi, SU Hangli, WANG Shuang, WANG Zhitao, BU Cancan, LV Wenxiang, WANG Xinmei, LIU Lijuan, SHENG Zhaoan, ZHANG Benguang. Sequencing and analysis of the complete mitochondrial genome of Rhipicephalus turanicus in Shandong Province[J]. Chinese Journal of Parasitology and Parasitic Diseases, 2025, 43(3): 377-384.

图/表 8

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基因 Gene	位置 Location	长度/bp Length/bp	起始密码子 Star codon	终止密码子 Stop codon	反密码子 Anticodon	编码链 Coding strand	基因间隔/bp Gene interval/bp
trnC	1~60	60	-	-	GCA	N	-
trnM	64~128	65	-	-	CAT	N	3
nad2	144~1 085	942	ATA	TAA	-	N	15
trnW	1 087~1 147	61	-	-	TCA	N	1
trnY	1 149~1 211	63	-	-	GTA	J	1
cox1	1 204~2 742	1 539	ATT	TAA	-	N	-8
cox2	2 747~3 422	676	ATG	T	-	N	4
trnK	3 420~3 486	67	-	-	CTT	N	-3
trnD	3 486~3 550	65	-	-	GTC	N	-1
ATP8	3 551~3 709	159	ATC	TAA	-	N	0
ATP6	3 703~4 368	666	ATG	TAA	-	N	-7
cox3	4 379~5 154	776	ATG	TA	-	N	10
trnG	5 157~5 219	63	-	-	TCC	N	2
nad3	5 217~5 561	345	ATA	TAG	-	N	-3
trnA	5 569~5 631	63	-	-	TGC	N	7
trnR	5 633~5 693	61	-	-	TCG	N	1
trnN	5 692~5 752	61	-	-	GTT	N	-2
trnS1	5 751~5 805	55	-	-	TCT	N	-2
trnE	5 808~5 869	62	-	-	TTC	N	2
nad1	5 868~6 809	942	ATA	TAA	-	J	-2
trnL2	6 807~6 868	62	-	-	TAA	J	-3
rrnL	6 869~8 060	1 191	-	-	-	J	0
trnV	8 063~8 122	60	-	-	TAC	J	2
rrnS	8 123~8 816	693	-	-	-	J	0
NCR1	8 817~9 118	301	-	-	-	N	0
trnI	9 119~9 181	63	-	-	GAT	N	0
trnQ	9 184~9 248	65	-	-	TTG	J	2
trnF	9 274~9 331	58	-	-	GAA	J	25
nad5	9 332~10 990	1 659	ATT	TAA	-	J	0
trnH	10 991~11 051	61	-	-	GTG	J	0
nad4	11 058~12 365	1 308	ATT	TAA	-	J	6
nad4L	12 368~12 643	276	ATG	TAA	-	J	2
trnT	12 646~12 706	61	-	-	TGT	N	2
trnP	12 707~12 770	64	-	-	TGG	J	0
nad6	12 758~13 207	450	ATA	TAA	-	N	-13
cytb	13 212~14 288	1 077	ATG	TAA	-	N	4
trnS2	14 289~14 351	63	-	-	TGA	N	0
trnL1	14 354~14 414	61	-	-	TAG	J	2
NCR2	14 415~14 718	304	-	-	-	N	0

区域 Region	长度/bp Length/bp	A含量/% A content/%	T含量 /% T content/%	G含量/% G content/%	C含量/% C content/%	A + T含量/% A + T content/%	AT偏斜值 AT-skew	GC偏斜值 GC-skew
全基因组 Complete sequence	14 718	37.8	40.1	9.9	12.3	77.8	-0.030	-0.108
蛋白质编码基因 Protein-coding gene	9 334	43.6	12.3	33.7	10.3	55.9	0.560	0.532
密码子第1位 First codon position	4 906	37.9	38.3	10.4	13.4	76.2	-0.005	-0.126
密码子第2位 Second codon position	4 906	35.7	41.9	9.7	12.6	77.6	-0.080	-0.130
密码子第3位 Third codon position	4 906	39.7	40.0	9.4	10.9	79.7	-0.004	-0.074
tRNA基因 tRNA gene	1 300	40.5	38.8	11.4	9.3	79.3	0.021	0.101
rRNA基因 rRNA gene	1 884	37.7	42.7	8.1	11.5	80.4	-0.061	-0.176

密码子（氨基酸） Codon (Amino acid)	数量/个 Number	密码子（氨基酸） Codon (Aminoacid)	数量/个 Number
UUU(F)	389	UAU(Y)	188
UUC(F)	121	UAC(Y)	56
UUA(L)	327	UAA(*)	290
UUG(L)	73	UAG(*)	53
CUU(L)	120	CAU(H)	81
CUC(L)	25	CAC(H)	15
CUA(L)	81	CAA(Q)	98
CUG(L)	26	CAG(Q)	24
AUU(I)	358	AAU(N)	317
AUC(I)	83	AAC(N)	66
AUA(M)	251	AAA(K)	321
AUG(M)	64	AAG(K)	65
GUU(V)	61	GAU(D)	57
GUC(V)	13	GAC(D)	16
GUA(V)	54	GAA(E)	81
GUG(V)	10	GAG(E)	25
UCU(S)	73	UGU(C)	41
UCC(S)	40	UGC(C)	14
UCA(S)	97	UGA(W)	75
UCG(S)	17	UGG(W)	25
CCU(P)	52	CGU(R)	13
CCC(P)	23	CGC(R)	2
CCA(P)	55	CGA(R)	23
CCG(P)	12	CGG(R)	8
ACU(T)	79	AGU(S)	56
ACC(T)	18	AGC(S)	21
ACA(T)	44	AGA(S)	72
ACG(T)	12	AGG(S)	30
GCU(A)	45	GGU(G)	30
GCC(A)	15	GGC(G)	6
GCA(A)	34	GGA(G)	47
GCG(A)	3	GGG(G)	15

山东图兰扇头蜱线粒体基因组全序列测定与分析

Sequencing and analysis of the complete mitochondrial genome of Rhipicephalus turanicus in Shandong Province

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