The genus Ornithodoros is notably diverse within the family Argasidae, comprising approximately 134 species distributed among 4 subgenera, 1 of which is the subgenus Pavlovskyella. In an earlier study, we identified distinct soft ticks as Ornithodoros (Pavlovskyella) sp., which were collected from animal shelters in Khyber Pakhtunkhwa, Pakistan. Providing additional collections from that same locality and a comprehensive analysis involving detailed morphological and mitogenome-based comparisons with closely related species, this study formally designates a novel species for these specimens. Adults and late-instar nymphs of the new species display a dorsoventral groove, small cheeks not covering the capitulum, 5 small even humps on tarsus I and a transverse postanal groove intersecting the median postanal groove perpendicularly. It also lacks a tuft of setae on the ventral surface of the hood which separates the novel species from Ornithodoros papillipes. Ventral chaetotaxy of tarsus IV indicates 4–7 setal pairs in nymphs and 5–7 pairs in adults that separate the new species from Ornithodoros tholozani sensu stricto and Ornithodoros crossi, 2 morphologically closely related species that occur in geographical proximity. Phylogenetic analyses of the full-length mitochondrial genome and the 18S and 28S ribosomal RNA genes, combined with pairwise nucleotide comparisons of cox1, cox2, atp8, atp6, cox3, nad3, nad5, nad4, nad4L, nad6, cytb, nad1, nad2, 12S rDNA, 16S rDNA, 18S rDNA and 28S rDNA further support that the new species belongs to the Pavlovskyella subgenus, clustering with O. tholozani, Ornithodoros verrucosus and Ornithodoros tartakovskyi.

Trematodes of the family Allocreadiidae are primarily found in the intestines of freshwater fishes around the world. The family includes 15 genera and c. 130 species. The last 2 decades have witnessed an increase in the genetic library of its species. Molecular data have been crucial for species delimitation and species description within Allocreadiidae and for understanding their evolutionary and biogeographical history and classification. Here, the mitogenomes of 3 species of allocreadiids were obtained using high throughput sequencing methods. Mitogenomes were compared with other members of the order Plagiorchiida to determine their molecular composition, gene rearrangement and phylogenetic interrelationships. The complete circular mitogenomes of Allocreadium lobatum, Creptotrematina aguirrepequenoi and Wallinia mexicana were 14 424, 13 769 and 13 924 bp long respectively, comprising 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. Gene arrangements were identical to other Xiphidiatan trematodes. Phylogenetic analyses using the mitogenomes revealed Allocreadiidae as a monophyletic group closely related to other members of the suborder Xiphidiata; A. lobatum was yielded as the sister taxon of C. aguirrepequenoi + W. mexicana. Our study increases the complete mitochondrial genome library of trematodes and strengthens our understanding of the phylogenetic relationships and classification of this parasite group.

The alvinocaridid shrimp Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, is an evolutionarily important deep-sea species in hydrothermal vents of north-western Pacific. A genome survey of S. leurokolos was carried out in order to provide a foundation for its whole-genome sequencing. A total of 599 Gb high-quality sequence data were obtained in the study, representing approximately 118× coverage of the S. leurokolos genome. According to the 17-mer distribution frequency, the estimated genome size was 5.08 Gb, and its heterozygosity ratio and percentage of repeated sequences were 2.85 and 87.03%, respectively, showing a complex genome. The final scaffold assembly accounted for a total size of 9.53 Gb (32,796,062 scaffolds, N50 = 597 bp). Repetitive elements nearly constituted 45% of the nuclear genome, among which the most ubiquitous were long interspersed nuclear elements, DNA transposons and long-terminal repeat elements. A total of 12,121,553 genomic simple sequence repeats were identified, with the most frequent repeat motif being di-nucleotide (70.27%), followed by tri-nucleotide and tetra-nucleotide. From the genome survey sequences, the mitochondrial genome of S. leurokolos was also constructed and 71 single nucleotide polymorphisms were identified by comparison with previous published reference. This is the first report of de novo whole-genome sequencing and assembly of S. leurokolos. These newly developed genomic data contribute to a better understanding of genomic characteristics of shrimps from deep-sea chemosynthetic ecosystems, and provides valuable resources for further molecular marker development.

The increasing use of massively parallel sequencing in the study of current and ancient human populations has enabled new approaches to bioanthropological and archaeological issues; however, its application to archaeological samples requires the use of technologies that are not easily accessible outside US and European research centers. To obtain an ancient mitogenome in Argentina, several institutions collaborated to apply massively parallel sequencing and bioinformatic methodologies on an enriched ancient DNA library of an individual from the Beagle Channel (dated 1504 ± 46 years BP), a region of particular interest for this line of inquiry. Phylogenetic reconstruction showed a close relationship with a Yamana from Navarino Island and an individual from Hoste Island (Chilean Antarctic Province): the three shared an ancestor who lived between 203 and 4,439 years ago. These three have mutations reported only for current and ancient individuals from the Beagle Channel, and their relationship with the rest of the D1g sub-haplogroups is unclear. The results obtained here are consistent with the reduction of mobility in the Fuegian archipelago around 4500 years BP that has been proposed based on archaeological evidence.

The annelid mitochondrial genomes (mitogenomes) have been well documented, and phylogenetic analyses based on the mitogenomes provide insightful implications for annelid evolution. However, the mitogenomes of some families remain unknown. Herein, we determined the complete mitogenome of the lugworm Abarenicola claparedi oceanica (15,524 bp), representing the first mitogenome from the family Arenicolidae. The gene order of this species is the same as the various lineages in Sedentaria. The maximum likelihood phylogenetic analyses were performed based on six different datasets, including 43 ingroups (oligochaetes, hirudineans, echiurans and closely related polychaetes) and two outgroups (Siboglinidae), namely, aligned and trimmed datasets consisting of the nucleotide sequences of protein-coding genes (PCGs) and rRNAs, and amino acid sequences of PCGs. Phylogenetic analyses based on the nucleotide sequences yielded trees with better support values than those based on the amino acid sequences. Arenicolidae is clustered with Maldanidae in all analyses. Analyses based on nucleotide sequences confirm the monophyly of Terebellidae, which was paraphyletic in recent mitogenomic phylogenetic studies. We also performed the phylogenetic analysis based on the RY-coding of the nucleotide sequences of PCGs only to yield phylogeny with generally low support values. Additional mitogenome sequences of related ingroup species would be needed to comprehensively understand the phylogenetic relationship, which was not present in this study.

In this study, we report the first complete mitochondrial genome of the tapeworm Nippotaenia mogurndae in the order Nippotaeniidea Yamaguti, 1939. This mitogenome, which is 14,307 base pairs (bp) long with an A + T content of 72.2%, consists of 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two rRNA genes, and two non-coding regions. Most tRNAs have a conventional cloverleaf structure, but trnS1 and trnR lack dihydrouridine arms of tRNA. The two largest non-coding regions, NCR1 (220 bp) and NCR2 (817 bp), are located between trnY and trnS2 and between nad5 and trnG, respectively. Phylogenetic analyses of mitogenomic data indicate that N. mogurndae is closely related to tapeworms in the order Cyclophyllidea.

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T > G > C > A. Five Asian and American Paragonimus species and P. westermani had TTT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotremus. The P. westermani clade was clearly separate from remaining congeners. The latter clade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae.

We report the nearly complete mitochondrial genome of Rhabdosynochus viridisi – the first for this genus – achieved by combining shotgun sequencing of genomic and cDNA libraries prepared using low-input protocols. This integration of genomic information leads us to correct the annotation of the gene features. The mitochondrial genome consists of 13,863 bp. Annotation resulted in the identification of 12 protein-encoding genes, 22 tRNA genes and two rRNA genes. Three non-coding regions, delimited by three tRNAs, were found between the genes nad5 and cox3. A phylogenetic analysis grouped R. viridisi with three other species of diplectanid monogeneans for which mitochondrial genomes are available.

The order Onchoproteocephalidea (Eucestoda) was recently erected to accommodate the hook-bearing tetraphyllideans and the proteocephalideans, which are characterized by internal proglottization and a tetra-acetabulate scolex. The recognized subfamilies in the Proteocephalidae appeared to be non-monophyletic based on 28S recombinant DNA (rDNA) sequence data. Other molecular markers with higher phylogenetic resolution, such as large mitochondrial DNA fragments and multiple genes, are obviously needed. Thus the mitochondrial genome of Gangesia oligonchis, belonging to the putative earliest diverging group of the Proteocephalidae, was sequenced. The circular mitogenome of G. oligonchis was 13,958 bp in size, and contained the standard 36 genes: 22 transfer RNA genes, two rRNA genes and 12 protein-coding genes, as well as two major non-coding regions. A short NCR and a large NCR (lNCR) region were 216 bp and 419 bp in size, respectively. Highly repetitive regions in the lNCR region were detected with that of 11 repeat units. The mitogenome of G. oligonchis shared 71.1% nucleotide identity with Testudotaenia sp. WL-2016. Phylogenetic analyses of the complete mitochondrial genomes with Bayesian inference and maximum likelihood methods indicated that G. oligonchis formed a sister clade with Testudotaenia sp. WL-2016 with maximum support. The ordinal topology is (Caryophyllidea, (Diphyllobothriidea, (Bothriocephalidea, (Onchoproteocephalidea, Cyclophyllidea)))). The mitogenomic gene arrangement of G. oligonchis was identical to that of Testudotaenia sp. WL-2016. Both mitogenomic and nuclear sequence data for many more taxa are required to effectively explore the inter-relationships among the Onchoproteocephalidea.

Maruca vitrata (Fabricius, 1787) is a cryptic pantropical species of Lepidoptera that are comprised of two unique strains that inhabit the American continents (New World strain) and regions spanning from Africa through to Southeast Asia and Northern Australia (Old World strain). In this study, we de novo assembled the complete mitochondrial genome sequence of the New World legume pod borer, M. vitrata, from shotgun sequence data generated on an Illumina HiSeq 2000. Phylogenomic comparisons were made with other previously published mitochondrial genome sequences from crambid moths, including the Old World strain of M. vitrata. The 15,385 bp M. vitrata (New World) sequence has an 80.7% A+T content and encodes the 13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes in the typical orientation and arrangement of lepidopteran mitochondrial DNAs. Mitochondrial genome-wide comparison between the New and Old World strains of M. vitrata detected 476 polymorphic sites (4.23% nucleotide divergence) with an excess of synonymous substitution as a result of purifying selection. Furthermore, this level of sequence variation suggests that these strains diverged from ~1.83 to 2.12 million years ago, assuming a linear rate of short-term substitution. The de novo assemblies of mitochondrial genomes from next-generation sequencing (NGS) reads provide readily available data for similar comparative studies.