Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species

Abstract

Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

The complete mitochondrial genome of Eulaelaps huzhuensis (Mesostigmata: Haemogamasidae)

“…The rare start codon (GTG) has been reported in the mitochondrial genome of some species within the families Characidae, Agromyzidae, and Perlidae (Yang et al 2013 ; Brandao-Dias et al 2016 ; Cao et al 2019 ). In the use of stop codons, 10 protein-coding genes ended with the complete stop codon TAA/TAG (TAA:7, TAG:3) and three protein-coding genes ( nad4 , nad5 , cob ) had the incomplete stop codon T. Incomplete stop codons are a common feature of many metazoa (Liu et al 2019 , 2022 ). These incomplete stop codons can be formed into complete stop codons TAA after transcription by polyadenylation (Huang et al 2022 ).…”

First mitochondrial genome of Amblyomma triste Koch, 1844 (Acari: Ixodidae): Evidence for studying species within the A. maculatum group</p >

“…In both cases, these regions have a conserved location within the mitogenome (Montagna et al 2012; Kelava et al 2021). Alternatively, they may be specific to the group, for example, Metastriata and Australasian Ixodes (Prostriata) have two non-coding regions, but with different locations within the mitogenome (Montagna et al 2012; Liu et al 2022). Changes in the non-coding regions of the mitochondrial DNA suggest potential differences in replication/transcription mechanisms, as NCRs contain regulatory elements (Burger et al 2012; Liu et al 2013; Wang et al 2019; Chavatte & Octavia 2021).…”

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

“…ATP6, ATP8, COX2, Cytb, ND3, ND4L, and ND6 were terminated with the representative stop codon TAA or TAG, COX1, ND1, and ND5 ended with AGA or AGG, while COX3, ND2, and ND4 were occasionally terminated with the truncated stop codon TA or T (Table 2). The incomplete stop codons TA and T are common in metazoan mitogenomes [19,20,51,72], and they can be converted to TAA by post-transcriptional modifications during the mRNA maturation process [77]. The start and stop codons of the 13 PCGs were very similar in the mitogenomes of T. indicus and T. cyanurus, and the only difference was the stop codon of the ND6 gene: the former was TAG, while the latter was AGG (Table 2).…”

“…With the assistance of Sangon Biotech Co., Ltd. (Shanghai, China), we sequenced the mitochondrial genome through a high-throughput sequencing technique. Library preparation, mitogenome sequencing, and mitogenome assembly were performed as previously described [51]. Mitogenome annotations were implemented using MITOS Web-Server (http://mitos2.bioinf.uni-leipzig.de/index.py, accessed on 15 August 2023) [52] and MitoAnnotator (http://mitofish.aori.u-tokyo.ac.jp/annotation/input/, accessed on 15 August 2023) [53].…”

“…The AT-skew values of the entire genome, concatenated rRNAs, concatenated PCGs, and single rRNA and PCG (except ND6) were positive, while the GC-skew values were negative (Figure 5), as was common in mitogenomes of Strigiformes [18] and Accipitriformes [74], indicating that Cs were more abundant than Gs, and As were more abundant than Ts. AT-skew and GC-skew were due to the different distribution of nucleotides between the two DNA strands, which further led to an asymmetry in the DNA strands [51,80]. We also analyzed the correlation between nucleotide content and corresponding skew of all mitogenomes of Muscicapidae (Figure 5), but the correlation was weak and further confirmation was needed with more data.…”