Genomes 3 Ta Brown Pdf.44 UPD
Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.
genomes 3 ta brown pdf.44
Ticks are obligate blood-sucking arachnid ectoparasites that can feed on a wide range of vertebrates, including mammals, birds and reptiles [1, 2]. Ticks are well-known zoonotic pathogen vectors, and tick-borne diseases (TBDs) are increasingly threatening animal and human health, thereby causing great economic damage [3, 4]. Many important tick-borne pathogens have been characterized from ticks in recent years, including Anaplasma bovis, Babesia ovata, Rickettsia japonica, Chlamydiaceae bacteria and severe fever with thrombocytopenia syndrome virus (SFTSV), which have attracted increasing attention in the field of public health [5,6,7,8,9]. Recently, a newly segmented virus with a febrile illness similar in its clinical manifestation to tick-borne encephalitis virus (TBEV) was discovered, which was designated as Alongshan virus (ALSV) and confirmed in 86 patients from several provinces in China . Globally, the annual financial losses due to ticks and TBDs are in the billions of dollars [3, 11]. A total of 896 tick species have been described worldwide in three families: Ixodidae (hard ticks, 702 species), Argasidae (soft ticks, 193 species) and Nuttalliellidae (1 species) [12,13,14]. Hard ticks possess a sclerotized scutum in all life stages except eggs, have an apically located gnathostoma, usually feed for several days and ingest a large amount of blood [15, 16]. Soft ticks have no sclerotized scutum and mouthparts located anteroventrally. The ticks usually feed and expand the body within minutes to hours . Nuttalliella namaqua is the unique species in the family Nuttalliellidae, and it displays many characteristics associated with hard and soft ticks and can engorge as rapidly as soft ticks . The differences in life history, behaviour, and morphological characteristics are useful for the discrimination of soft ticks and hard ticks, but there are still numerous difficulties among the interspecies taxonomic characterization and geographical origin of ticks, especially for soft ticks . Therefore, the increasing number of characterized mt-genomes has shown considerable potential in tick phylogeny, molecular evolution and population genetics.
The first mt-genomes of ticks (Ixodes hexagonus and Rhipicephalus sanguineus) were reported by Black et al.  in 1998. As of May 2019, 63 complete tick mt-genomes have been deposited in the NCBI database. Most tick mt-genomes were published in this decade, and are from 3 families and 15 genera, including 35 species in the family Ixodidae: Ixodes (7 species); Amblyomma (7 species); Rhipicephalus (5 species); Rhipicentor (1 species); Dermacentor (4 species); Bothriocroton (2 species); Haemaphysalis (8 species); and Hyalomma (1 species) [26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41]; 27 species in the family Argasidae: Argas (8 species); Antricola (1 species); Carios (2 species); Ornithodoros (14 species); Otobius (1 species); and Nothoaspis (1 species) [19, 27, 42,43,44]; and 1 Nuttalliella species in family Nuttalliellidae  (Table 1). In recent years, phylogenetic studies based on mt-genome sequences have been effectively carried out for many tick species [21, 28,29,30, 36, 40]. These achievements are also essential for understanding the genetic differentiation and phylogeny of ticks [31,32,33,34]. However, the genera Anomalohimalaya, Compluriscutula, Margaropus and Nosomma still lack complete mt-genome information, and most species were sampled in a limited geographical area . Complete mt-genome sequences have only been obtained for approximately 7% (63/896) of the tick species, and the general characteristics of most tick mt-genomes remain to be determined.
The length of the mt-genomes of ticks average 14,633 bp, with the longest reaching 15,227 bp (Ixodes tasmani) and the smallest measuring only 14,307 bp (Argas boueti) (Table 2). Generally, the length of the mt-genomes from hard ticks is slightly longer than that of soft ticks (14,796 and 14,429 bp, respectively). The length differences of the mt-genomes between ticks may be influenced by gene rearrangement and the length of the non-coding regions (NCRs) [46, 47]. MITOS online analysis showed no gene deletion or duplication in tick mt-genomes, which contain 13 PCGs, 2 rRNA genes and 22 tRNA genes. Among the 13 PCGs, 9 PCGs (nad2, cox1, cox2, atp8, atp6, cox3, nad3, nad6, cytb) are located in the majority strand (J strand) and 4 PCGs (nad5, nad4, nad4L, nad1) are located in the minority strand (N strand).
The mitochondrial tRNA gene length in ticks ranges from 50 to 90 bp, and most tRNA genes have a complete cloverleaf structure, including four principal structures: amino acid acceptor (AA) arm; TΨC (T) arm; anticodon (AC) arm; and dihydrouridine (DHU) arm . No DHU arm structure exists in trnS1 of the tick mt-genomes; a similar phenomenon is also observed in insects [20, 65, 66]. The distance from the anti-codon to the CCA terminus is hence maintained through the inverted L structure, which helps complete the gene function . Additionally, base mismatches frequently occur in the secondary structure of the tick tRNA genes [68, 69]. The mismatch types are mainly G-U, U-G and U-U, which are similar to those of other insects [62, 70]. These mismatches may be related to the evolutionary mutations and may not affect the function of tRNA genes due to being corrected later .
The mitochondrial rRNA genes display a complex functional structure with a relatively slow evolution rate; these have long been used as population genetics markers . The tick mt-genomes contain two single copy 12S and 16S rRNA genes. In recent years, the mitochondrial 12S and 16S rRNA genes have been extensively used as genetic targets in phylogenetic research of ticks [27, 36, 73]. Due to gene rearrangement, the position of the rRNA genes shifts in ticks, whereas the gene order and the location in the N strand remain unchanged. Previous reports have shown that the average genetic distance of different tick taxa was still very slight even after tens of million years of evolution. Slow nucleotide variation in rRNA genes may be caused by strict structural and functional limitations . Therefore, to this end, using combined PCGs and rRNA genes to reconstruct the phylogenetic relationships and resolve the controversial genealogy of soft ticks may be one of the best methods .
The mt-genomes play an important role in the molecular systematics and origin of ticks. In the present study, 13 PCGs and 2 rRNA genes from the MITOS analysis results of all available tick complete mt-genomes were used to construct a phylogenetic tree through the maximum likelihood method (ML) . MEGA v.6.0 for Windows ( ) was first used for alignment and splicing, and then the IQ-Tree online server ( ) was used for establishment of the phylogenetic tree with 1000 bootstrap replications [84, 85]. The phylogenetic tree was constructed using the nucleotide sequences (12,150 bp) of 63 tick species. Limulus polyphemus (NC003057) was used as the outgroup and the percentage of the bootstrap support is given at each node.
In soft ticks, some species in Argas and Ornithodoros have previously been phylogenetically analyzed using 10 mitochondrial genes . Recently, several new mt-genomes have become available for the genus Argas including Ar. boueti, Ar. brumpti, Ar. persicus, Ar. striatus and Ar. walkerae, and for the genus Ornithodoros including O. compactus, O. coriaceus, O. costalis, O. hermsi, O. parkeri, O. sonrai, O. tholozani, O. turicata and O. zumpti. These were incorporated into the present phylogenetic analysis using 13 PCGs and 2 rRNA genes. Results yielded ambiguous species delimitation and phylogenetic relationships of these two genera (Fig. 2), which are complicated with the existing of monophyly, paraphyly, or polyphyly phenomena. Possibly, the concatenation of present genes with other informative genes help a better phylogenetic resolution. The tick Ar. boueti was clustered within the subfamily Ornithodorinae with a minimum bootstrap of 51%. This clustering may influence the location of other genera, including Antricola, Nothoaspis and Carios. Additionally, the tick Carios faini was clustered first with Antricola mexicanus and Nothoaspis amazoniensis, as well as with C. capensis. Subsequently, the incongruence was apparent between phylogenetic configurations and morphological characterizations, which requires further evidential confirmation.