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

doi:10.12140/j.issn.1000-7423.2025.03.012

Abstract

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

CLC Number:

R384.41

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.

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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