The Complete Mitogenome of Haemaphysalis parva (Arachnida: Ixodidae) and Comparative Mitogenomics of Haemaphysalis Species
Habeş Bilal Aydemir, Adem Keskin
TL;DR
This paper reports the complete mitochondrial genome of Haemaphysalis parva, a tick species that can transmit diseases, and compares it with other Haemaphysalis species to understand their genetic structure and evolution.
Contribution
The study provides the first complete mitogenome of Haemaphysalis parva and identifies lineage-specific features through comparative analysis.
Findings
The mitogenome of H. parva is 14,843 bp and contains 37 canonical genes and two non-coding regions.
Several genes show signs of positive selection, indicating adaptive evolution in this tick species.
Comparative analysis reveals a rearranged gene block and conserved sequence blocks, including a putative humanin-like ORF.
Abstract
Introduction Ticks are globally recognised as the second most important vectors of infectious diseases, posing significant threats to human and animal health. Haemaphysalis parva (Acari: Ixodidae) is frequently reported infesting humans and domestic animals and has been experimentally demonstrated to transmit Babesia ovis, with field associations to ovine babesiosis during the colder months. It has also been reported to harbour several zoonotic pathogens, including Coxiella burnetii, Francisella tularensis, and various Rickettsia species. Here, we aim to report the complete mitochondrial genome of Haemaphysalis parva (Ixodida: Ixodidae), a zoonotic tick species with significant public health relevance in Türkiye. Methods For this purpose, we isolated total genomic DNA from H. parva and sequenced using Illumina HiSeq 2000 platform, raw reads were processed, and then the mitogenome was…
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5- —Tokat Gaziosmanpasa University
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsVector-borne infectious diseases · Genomics and Phylogenetic Studies · Invertebrate Immune Response Mechanisms
Introduction
In terms of genome structure and gene content, animal mitogenomes are stable and predictable in eukaryotic groups [7, 37]. In bilateral animals, the mitogenome is generally fixed with 37 genes: 13 protein-coding genes (PCGs) that code subunits of the electron transport chain, two ribosomal RNA (rRNA) genes involved in the translation of these PCGs, and 22 transfer RNA (tRNA) genes [26]. PCGs constitute the subunits of four of the five mitochondrial complexes embedded in the mitochondrial inner membrane that are involved in oxidative phosphorylation. Of these genes, NADH dehydrogenase subunit 1 (nd1), nd2, nd3, nd4, nd4L, nd5 and nd6 encode the proteins of complex 1 (NADH-ubiquinol oxidoreductase); cytochrome b (cytb) complex 3 (ubiquinone-cytochrome-c-oxidoreductase); cytochrome-c-oxidase subunit 1 (cox1), cox2 and cox3 complex 4 (cytochrome-c-oxidase); and finally ATP synthase Fo subunit 6 (atp6) and atp8 complex 5 (ATP synthase). Two rRNA genes encode the large (16S) and small (12S) subunit genes participating in ribosome structure; 22 tRNA genes encode tRNA molecules with one copy for each amino acid, except for serine and leucine, which have two copies [12]. In addition to the coding gene content, the mitogenome contains one or more non-coding regions. These regions function as binding sites for proteins involved in genome replication or transcription. The major non-coding region is called the major control region or displacement loop (D-loop) [32].
Over the last 50 years, numerous total mitochondrial genome sequences have been obtained, and many studies have evaluated genome structure, gene content, organization, and expression from different perspectives. Comparative mitochondrial genome studies allow assessment of mitochondrial genome variations from both general (supra-species level) and specific (intra-species and gene level) perspectives [2]. The fact that the mitogenome has emerged only once in the evolutionary process makes mitogenome data a unique resource for evolution and mutation studies. Phylogenetic trees constructed with genes encoded from nDNA and mtDNA show strikingly similar constructions [31].
Therefore, studies about small, circular, and simple mtDNA are easier than studies with large, chromosome-packaged, and highly complex nDNA. Mitogenome-level rearrangement patterns are also being used as a new source for both phylogenetic and evolutionary biology studies [8]. Nuclear mtDNA remnants (NUMTs) are informative in mutational and evolutionary processes. Horizontal and lateral gene transfers, genetic code differences, asymmetric replication and transcription processes, and transcriptome studies are also used mtDNA as a template for many studies [12].
Ticks are worldwide arthropod parasites that feed on blood from terrestrial vertebrates and are vectors of various diseases. Ticks, particularly those parasitizing humans, play a significant role in the transmission of viral, rickettsial, bacterial, and protozoan diseases to humans [9, 19, 20]. Mitochondrial genomes have provided substantial insights into the evolutionary history, population genetics, and phylogeography of mites and particularly strong contributions to studies on ticks. Currently, more than 300 complete mitochondrial genomes for 125 tick species are available in the NCBI database, and mitogenomic studies on ticks are expanding rapidly as new species are sequenced each year [3, 11, 34, 36].
Haemaphysalis parva is a hard tick species distributed in the Palearctic region, with a particular prevalence in the Mediterranean Basin and Middle East. This species is especially active during the autumn months and primarily infests livestock. It also parasitizes a range of wild animals, including wild boars, rabbits, foxes, Eurasian lynx, as well as both domestic and wild horses [35]. H. parva can occasionally infest humans and is recognized as a vector of several zoonotic agents, including Coxiella sp., Francisella tularensis subsp. holarctica, Babesia spp., and Hepatozoon spp., with a particular association with Rickettsia species such as R. massiliae and ‘Candidatus Rickettsia goldwasserii’ [41]. In this study, the total mitochondrial genome of Haemaphysalis parva (Ixodida: Ixodidae), a species that frequently infects humans in Türkiye, was sequenced and compared with other Haemaphysalis species, whose mitogenome data are available in the NCBI database.
Materials and Methods
Sampling of Haemaphysalis parva and DNA extraction
Haemaphysalis parva species were collected from infected humans in Tokat province (40° 19’ North and 36° 43’ East) and stored in Tokat Gaziosmanpaşa University, Department of Biology, Parasitology research laboratory in Tokat (Türkiye) between 2009 and 2011. Species were preserved in − 20 °C in 100% ethanol and was identified at the species level using morphological characteristics via various species identification keys [13, 14] under a stereomicroscope (Leica MZ16 and Olympus SZ61). All specimens were preserved in 100% ethanol at − 20 °C before molecular analyses. In addition to the specimens used in this study, tick specimens collected from humans in the same localities are preserved in the Tokat Gaziosmanpaşa University, Department of Biology, Parasitology Research Laboratory in Tokat (Türkiye), providing a reference material for future taxonomic verification. The universal cox1 barcode region was amplified for verification of morphological characterization and identification molecularly via BOLD system after DNA extraction (as detailed in the following paragraph).
Total DNA was extracted from the leg set of selected organisms using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s instructions with minor changes. The extracted DNA were measured qualitatively and quantitatively via agarose gel electrophoresis and MicroDrop (Invitrogen), respectively.
The universal cox1 barcode region was amplified for verification of morphological characterization and identification molecularly via BOLD system after DNA extraction and PCR. For amplification of cox1 barcode region cox1-F 5′-AATGTAATTGTAACTGCTCATGC-3′ and cox1-R 5′-CTATTCCTACTGTAAATATRTGATG-3′ primers were designed, synthesized, and used with 45 °C annealing temperature in Biorad T-100 thermal cycler. A 729 bp long amplicon were sequenced using Standart Sanger sequencing, conducted at Macrogen Inc. (Netherlands). Reads were initially proceeded with end-trimming and assembling. After the consensus cox1 sequence was generated and searched in BOLD System v3 [27], the species has been confirmed to be Haemaphysalis parva.
Sequencing and Data Analysis
The total of 100 ng of the extracted DNA was sequenced as 150 bp paired end reads using Illumina HiSeq 2000 platform (Macrogen Inc. (Netherlands)) to generate ~ 66 million high quality reads, 10 GB raw data. Raw NGS reads were filtered qualitatively using FastQC v0.11.4 (http://www.bioinformatics.babraham. ac.uk/projects/fastqc). The filtered high-quality reads were assembled into contigs with “map to reference” option in Geneious R9 using other Haemaphysalis RefSeq data in NCBI (NC_085275, NC_037246, NC_039765, NC_037493) under the parameters of ‘medium–low sensitivity’ and ‘iterate up to five times’ [18]. After consensus sequences were generated, BLASTn search was conducted. The assemblies with a high score that matched Haemaphysalis mitogenomes were fully annotated to provide a final assembly.
Mitogenome Characterization of Haemaphysalis parva
For the standard characterization of mitogenomes, organizations of the PCGs were identified using ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder) and MITOS (http://mitos2.bioinf.uni-leipzig.de/index. py) with the invertebrate mitochondrial genetic code prior [5]. Amino acid sequences of the putative ORFs were verified with BLASTp. Conserved domains of protein coding genes were determined via BLAST CD-search [24]. tRNA genes were annotated with tRNA-Scan SE and ARWEN servers under the mito/chloroplast genetic code and the default search options [22, 23]. The precise ends of rRNA genes were determined based on the locations of adjacent genes and their putative secondary structures were constructed according to the commonly accepted comparative approach and algorithm-based methods. XRNA 1.2.0b (http://rna.ucsc.edu/rnacenter/xrna/xrna.html) was used to draw the folding structure with the results of the CRW site as reference [10]. Intergenic spacers and overlapping regions were determined manually. The boundary of the A + T-rich region was determined by considering the adjacent genes. The number, position and length of the repeated sequence motifs were searched by Tandem Repeat Finder v4.07b using default setting under basic option [4]. Finally, the whole mitogenome sequence of Haemaphysalis parva was deposited in the GenBank under accession number PX122095.
Nucleotide and amino acid compositions of genes and mitogenomes were calculated and strand asymmetry values of each genomic compartment and each gene were counted using the following formulae: AT-skew = (A − T) / (A + T); GC skew = (G − C) / (G + C) [15].
Comparative Analysis of Haemaphysalis Mitogenomes
Complete mitogenome sequence of Haemaphysalis parva obtained from this study, and 26 different Haemaphysalis and mitogenome sequences from NCBI were used for comparative analyses (Table 1). Ixodes columnae (Arachnida: Ixodidae) were included in comparative analysis for determination of rearrangement events. For comparison of PCGs, relative synonymous codon usage (RSCU) value of genes was calculated with MEGA 11 software [33]. The ratio of the nonsynonymous substitution rate (dN) to the synonymous substitution rate (dS) was calculated with DNAsp v6 [28]. To assess the selective pressures acting on the analyzed protein-coding genes, the ratio of nonsynonymous to synonymous substitution rates (dN/dS, ω) was calculated. The dN/dS ratio provides a widely used measure for distinguishing between purifying, neutral, and positive selection acting at the protein level by comparing the rates of amino acid–altering and silent substitutions [38].Table 1. Mitogenome sequences and nucleotide characters which used in comparative analysis SpeciesAT%AT-skewAccession numberGenome lenghtTCAGGC%GC-skewPurine_Pyrimidine BiasAmino_Keto BiasAT_GC BiasNBHaemaphysalis parva 77,8− 0,010879972PX122095**14,843 39,3 12,8 38,5 9,5 22,2 − 0,147031963 − 4,12,455,5 2,09283 Haemaphysalis flava76,9− 0,018149624NC_00529214,68639,212,937,810,223,1− 0,115,895,016− 4,11,353,81,984,753Haemaphysalis formosensis78,3− 0,013577023NC_02033414,67639,712,438,69,321,7− 0,140,615,191− 4,12,056,62,19,572Haemaphysalis inermis78,8− 0,007690993NC_02033514,84639,712,139,19,021,2− 0,146,310,433− 3,72,557,62,251,718Haemaphysalis concinna78,0− 0,009875033NC_03478514,67539,412,838,69,222,0− 0,16,382,781− 4,42,856,02,154,286Haemaphysalis japonica77,6− 0,016062495NC_03724614,68539,412,638,29,822,4− 0,125− 4,01,555,32,09461Haemaphysalis longicornis77,2− 0,010567101NC_03749314,71839,013,138,29,822,8− 0,143,367,043− 4,12,554,32,019866Haemaphysalis hystricis77,2− 0,006335797NC_03976514,71638,912,938,49,822,8− 0,136,038,186− 3,62,654,42,027621Haemaphysalis bancrofti78,4− 0,010698443NC_04107614,67339,612,238,89,421,6− 0,130,352,645− 3,72,056,72,203,575Haemaphysalis montgomeryi78,50,004861955NC_05831214,68139,012,639,49,021,5− 0,169,143,218− 3,34,056,92,224,394Haemaphysalis sulcata76,4− 0,011145787NC_06206314,67938,613,737,89,923,6− 0,160,508,083− 4,62,952,81,919,978Haemaphysalis punctata78,0− 0,005320541NC_06206414,69739,212,738,89,222,0− 0,158,872,716− 3,93,156,12,154,409Haemaphysalis danieli81,1− 0,014060931NC_06206514,73941,110,740,08,218,9− 0,131,494,088− 3,61,462,12,628,976Haemaphysalis tibetensis77,7− 0,011801731NC_06206614,71539,312,738,49,622,3− 0,13,980,464− 4,02,255,52,105,623Haemaphysalis qinghaiensis77,5− 0,015725204NC_06206714,68339,412,738,29,822,5− 0,129,090,909− 4,11,755,12,077448Haemaphysalis doenitzi77,4− 0,009595915NC_06215814,67139,113,038,39,622,6− 0,153,381,643− 4,22,754,82,067735Haemaphysalis campanulata78,2− 0,003483714NC_06215914,69139,212,338,99,521,8− 0,127,454,036− 3,12,556,32,169,252Haemaphysalis yeni78,0− 0,012820513NC_06216014,69039,512,638,59,422,0− 0,145,454,545− 4,22,256,02,150,088Haemaphysalis kitaokai77,30,000865951NC_06216114,93638,613,138,79,522,7− 0,158,205,431− 3,53,754,62,015628Haemaphysalis cornigera78,1− 0,013172817NC_06216214,68139,612,338,59,621,9− 0,124,922,312− 3,81,756,22,160,052Haemaphysalis mageshimaensis78,1− 0,012356422NC_06216314,72139,512,538,69,421,9− 0,139,671,725− 4,02,156,12,154,261Haemaphysalis colasbelcouri78,0− 0,008532276NC_06216414,88539,312,738,69,322,0− 0,156,002,438− 4,12,855,92,115,937Haemaphysalis nepalensis77,8− 0,010572302NC_06412414,72039,312,738,59,522,2− 0,145,038,168− 4,02,455,52,107,832Haemaphysalis bispinosa78,7− 0,013965517NC_07176514,73239,912,038,89,221,3− 0,130,906,769− 3,91,757,52,254,885Haemaphysalis warburtoni77,8− 0,015650957NC_08420414,69539,512,638,39,622,2− 0,136,279,926− 4,21,855,72,122,546Haemaphysalis taiwana78,2− 0,012805994NC_08527514,68539,612,338,69,521,8− 0,128,509,046− 3,81,856,32,173,331Haemaphysalis novaeguineae78,0− 0,017369294NC_08788014,68139,712,338,39,622,0− 0,122,828,784− 4,11,3 56,12,154,562The bold value indicates the GenBank accession number of Haemaphysalis parva mitogenome data generated in this study and deposited in NCBI
Gene rearrangement events in Haemaphysalis were heuristically evaluated via CREx and qMGR with an Ixodidae reference, Ixodes columnae (NC_067861) [6, 40].
Collinearity analysis were conducted to compare Haemaphysalis species with riparian plot using pyGenomeViz v1.6.1 (https://pygenomeviz.streamlit.app/).
Results and Discussion
Mitogenome of Haemaphysalis parva
The Haemaphysalis parva complete mitogenome was annotated as 14,843 bp-long and can be accessed from NCBI under accession number PX122095. The mitogenome was visualized and given in Fig. 1, and the mitogenome feature table was given in Table 2. In the mitogenome, overall lengths of PCGs, tRNAs, and rRNAs are 10,749, 1354 and 1969 bp, respectively. Two major non-coding regions were determined between rrnS-trnI and trnL1-trnC genes with 312 and 304 bp long, respectively. The intergenic regions were 238 bp in total length and determined between 12 adjacent genes, except for major non-coding regions. On the other hand, the overlapping regions were dispersed among different gene junctions 101 bp in total length (Table 2). 15 neighbouring genes overlapped with from 1 to 23 nucleotides (Table 2). Conserved atp6-atp8 and nd4-nd4L overlaps were determined as 7 bp conserved length. The conserved and newly determined transcriptional sequence “WHWGHTW” identified in Ecdysozoa was detected in H. parva mitogenome immediately upstream (positions 12,647–12,653) of the nd4L gene [1].Fig. 1. Mitochondrial genome visualization of Haemaphysalis parva (Ixodida: Ixodidae)Table 2. Summary of mitochondrial genome of Haemaphysalis parvaNameMinimumMaximumLengthDirectionintergenic/overlappingstart codonstop codonanticodonT%C%A%G%AT-skewGC-skewtrnM(cat)26463forward− 12CAT29,714,142,214,10,173,9130nad2531024972forward− 2ATTTAA45,19,640,25,1− 0,05797− 0,3007trnW(tca)1023108361forward− 2TCA37,78,249,24,90,132,075− 0,25trnY(gta)1082114362reverse− 8GTA40,38,133,917,7− 0,086960,375cox1113626741539forward4ATTTAA38,615,532,513,4− 0,08592− 0,07416cox226793353675forward0ATGTAG37,515,637,39,6− 0,00198− 0,23,529trnK(ctt)3354341865forward− 1CTT36,913,835,413,8− 0,021280trnD(gtc)3418348164forward0GTC35,97,848,47,80,148,1480atp834823637156forward− 7ATCTAA42,312,242,92,60,007519− 0,65,217atp636314296666forward3ATGTAA48,012,232,37,5− 0,19,626− 0,23,664cox343005086786forward− 9ATGT—44,713,130,211,9− 0,19,322− 0,04569trnG(tcc)5078514164forward0TCC37,57,848,46,30,127,273− 0,11,111nad351425480339forward− 2ATTTAG50,19,131,39,4− 0,23,1880,015873trnA(tgc)5479554062forward1TGC38,79,743,58,10,058824− 0,09091trnR(tcg)5542560160forward− 1TCG40,011,735,013,3− 0,066670,066667trnN(gtt)5601566161forward9GTT32,813,137,716,40,0697670,111,111trnS1(tct)5671572656forward4TCT37,510,744,67,10,086957− 0,2trnE(ttc)5731579161forward0TTC44,39,834,411,5− 0,1250,076923nad157926724918reverse0ATTT—43,79,534,812,0− 0,11,3540,114,428trnL2(taa)6725678561reverse22TAA34,49,839,316,40,0666670,25rrnL680880751268reverse835,910,140,014,00,0552550,16,041trnV(tac)8084814259reverse− 9TAC39,011,939,010,20− 0,07692rrnS81348834701reverse31238,18,939,613,40,0183820,205,128trnI(gat)9147921165forward1GAT41,57,736,913,8− 0,058820,285,714trnQ(ttg)9213927967reverse3TTG43,34,540,311,9− 0,035710,454,545trnF(gaa)9283934361reverse− 1GAA39,34,947,58,20,094340,25nad5934310,9981656reverse0ATTTAA45,87,636,210,4− 0,11,7170,157,191trnH(gtg)10,99911,06365reverse− 23GTG44,61,543,110,8− 0,017540,75nad411,04112,3781338reverse− 7ATGTAA48,88,530,012,7− 0,23,9090,197,183nad4l12,37212,647276reverse2ATGTAA49,36,934,49,4− 0,17,7490,155,556trnT(tgt)12,65012,70960forward0TGT40,08,341,710,00,0204080,090909trnP(tgg)12,71012,77061reverse− 15TGG39,34,941,014,80,0204080,5nad612,75613,103348forward180ATATAA45,612,331,910,2− 0,17,736− 0,09091cytB13,28414,3631080forward− 1ATGTAG44,113,831,810,4− 0,16,239− 0,14,176trnS2(tga)14,36314,42563forward− 1TGA42,97,939,79,5− 0,038460,090909trnL1(tag)14,42514,48460reverse304TAG36,78,340,015,00,0434780,285,714trnC(gca)14,78914,84153forward1GCA35,87,550,95,70,173,913− 0,14,286
Haemaphysalis H parva mitogenome consists of T% = 39,3, A% = 38,5, C% = 12,8 and G% = 9,5 of nucleotides; indicating the negative AT- and negative GC-skewness values. Like other invertebrates, the mitogenome of H. parva was also biased to A + T nucleotides (%77,8). All PCGs, except atp8, show negative AT-skew, and; except L- strand encoded nd1, nd4, nd4L, nd5, and H-strand encoded nd3 genes, show negative GC-skew.
Both rrnL and rrnS genes have positive AT- and positive GC-skewness values. Most of the tRNA genes show positive AT- and positive GC-skew values, except trnK, trnY, trnE, trnR, trnI, trnQ, trnH and trnS2 which have negative AT-skewness value, and except for trnW, trnG, trnA, trnS1, trnV and trnC which shown negative GC-skewness.
Each protein-coding gene was biased towards having a high AT content, with hydrophobic amino acids, including isoleucine (13.69%), leucine (13.64%), phenylalanine (11.23%), and serine (10.22%). On the other hand, the existences of cysteine (0.92%), arginine (1.34%), and glutamine (1.42%) amino acid levels were the lowest (Table S1, Fig. 2).Fig. 2. Aminoacid compositions of Haemaphysalis parva mitochondrial PCGs
Initiation codons of cox2, cox3, cytB, atp6, nd4, and nd4L genes were standard ATG- methionine codon; cox1, nd1, nd2, nd3 and nd5 genes were started with ATT- isoleucine codon; nd6 and atp8 genes were found to initiate with ATA- methionine and ATC- isoleucine codons, respectively.
While atp6, atp8, cox1, nd2, nd4, nd4L, nd5, and nd6 genes have complete TAA stop codons; cox2, cytB, and nd3 genes terminate with TAG codon; and cox3 and nd1 genes have incomplete T—stop codons supposed to be completed with polyadenylation.
Comparative Mitogenomics of Haemaphysalis Species
Total length of Haemaphysalis mitogenomes varies from 14,671 (H. doenitzi) to 14,936 (H. kitaokai); with an average of 14,722 bp. There is no significant length variation within Haemaphysalis species (p > 0.001). Total nucleotide compositions of the Haemaphysalis mitogenomes are A and T-rich, with an 78% A + T content on average (Table S2). The arthropod mitogenomes commonly display positive AT and negative GC skew values, because the asymmetric nature of replication and transcription processes induces deamination mutations [29]. However, all analysed Haemaphysalis species show negative AT and GC-skewness values (Table S2). The existence of multiple replication origins may be interpreted as a skewness bias. Although rearrangement events are not detected between Haemaphysalis mitogenomes, nd1-rrnS gene block were rearranged in Haemaphysalis species when comparing the reference Ixodes mitogenome (Fig. 3).Fig. 3. Riparian plot representation of mitogenome sequences of Haemaphysalis parva and Ixodes columnae using BlastProtein genome comparison method
Comparisons of the RSCU values of degenerate codons revealed a significant correlation between codon preference and nucleotide composition. The most frequently used codons were counted as AUU (I), UUU (F), UUA (L2), AUA (M), AAU (N) and AAA (K) codons, which all of them have only A and U nucleotides. As expected for determinants in nucleotide compositions, both two-fold and four-fold degenerated codons are biased specifically to A and U nucleotides (Fig. 4).Fig. 4. Relative synonymous codon usage (RSCU) of the Haemaphysalis mitogenomes. Amino acids are provided on the x axis with alternative 3rd codon positions with different colors
The ratios of nonsynonymous to synonymous substitution rates (ω: dN/dS) between Haemaphysalis species in the mitochondrial PCGs are just about 1. Although dN/dS is generally less than 1, for some genes (cox1, cytB, nd2 and nd6) the average dN/dS ratio is higher than 1 (p < 2.2e-16) (Fig. 5). ω values support that mitogenomes of Haemaphysalis species are still evolved and not saturated yet. The overgeneralized guess about mitogenome evolutions have some handicaps.Fig. 5. Schematic representations of dN/dS (ω) values of mitochondrial PCGs of Haemaphysalis. For each gene, the bottom and top of the line indicates the minimum and maximum values, respectively
Collinearity analysis was conducted by comparing the mitogenome of H. parva (represented identical organized Haemaphysalis species) with reference Ixodes columnae mitogenomes. Three locally collinear blocks (LCBs) and numerous collinear blocks were identified, as illustrated in Fig. 3. In this study, using the MUMmer protein comparison method, the coding capacity of rrnL gene (probably the humanin-like gene) was detected as conserved sequence block (Fig. 3). Some sequence blocks represented in non-PCGs are conserved and may indicate conserved functional regions like replication- transcription origins or nuclear peptides like humanin and/or MOTS-c.
Conclusion
The complete mitochondrial genome of Haemaphysalis parva shows typical features of tick mitogenomes in terms of size, gene content, and high A + T bias. However, the consistent negative AT- and GC-skew values across all analyzed Haemaphysalis species deviate from the common arthropod pattern, suggesting alternative replication or transcription dynamics, possibly due to multiple replication origins [16, 30].
Codon usage was strongly influenced by nucleotide composition, favoring A + T-rich codons and hydrophobic amino acids, consistent with selective pressures on mitochondrial translation efficiency [25]. Overlapping gene regions and highly biased codon usage patterns may reflect genome compaction and regulatory complexity in mitochondrial gene expression.
Notably, some protein-coding genes (e.g., cox1, cytB, nd2, nd6) exhibited dN/dS ratios above 1, indicating potential positive selection and ongoing adaptive evolution in certain lineages. Additionally, the identification of conserved non-coding motifs and a putative humanin-like sequence within the rrnL gene points to functional elements beyond canonical OXPHOS-related genes [17, 21, 39].
Despite overall structural conservation, collinearity analysis revealed rearrangements (e.g., nd1–rrnS block) compared to Ixodes, supporting the utility of mitochondrial architecture in phylogenetic studies. These findings contribute valuable insight into the evolution, structure, and functional potential of tick mitogenomes and highlight the importance of further comparative and functional analyses across broader taxa.
Supplementary Information
Below is the link to the electronic supplementary material.Supplementary file1 (PDF 186 KB). Figure S1: Collinearity analysis of mitogenome sequences of Haemaphysalis parva and Ixodes columnae using (a) BlastNucleotide and (b) MummerProtein genome comparison methods.Supplementary file2 (XLS 30 KB)Supplementary file3 (XLSX 16 KB)
The reference list from the paper itself. Each links out to its DOI / PubMed record.
- 1Vatansever Z (2017) Haemaphysalis parva (Neumann 1897) (Figs 100–102). In: Ticks of Europe and North Africa. Springer International Publishing, Editors: Agustín Estrada-Peña, Andrei Daniel Mihalca, Trevor N. Petney, Cham, pp. 259–263