Fragmented mitochondrial genomes evolved in opposite directions between closely related macaque louse Pedicinus obtusus and colobus louse Pedicinus badii

Characterization of the fragmented mitochondrial genome of domestic pig louse Haematopinus suis (Insecta: Haematopinidae) from China

The domestic pig louse Haematopinus suis (Linnaeus, 1758) (Phthiraptera: Anoplura) is a common ectoparasite of domestic pigs, which can act as a vector of various infectious disease agents. Despite its significance, the molecular genetics, biology and systematics of H. suis from China have not been studied in detail. In the present study, the entire mitochondrial (mt) genome of H. suis isolate from China was sequenced and compared with that of H. suis isolate from Australia. We identified 37 mt genes located on nine circular mt minichromosomes, 2.9 kb-4.2 kb in size, each containing 2-8 genes and one large non-coding region (NCR) (1,957 bp-2,226 bp). The number of minichromosomes, gene content, and gene order in H. suis isolates from China and Australia are identical. Total sequence identity across coding regions was 96.3% between H. suis isolates from China and Australia. For the 13 protein-coding genes, sequence differences ranged from 2.8%-6.5% consistent nucleotides with amino acids. Our result is H. suis isolates from China and Australia being the same H. suis species. The present study determined the entire mt genome of H. suis from China, providing additional genetic markers for studying the molecular genetics, biology and systematics of domestic pig louse.

The fragmented mitochondrial genomes of two Linognathus lice reveal active minichromosomal recombination and recombination hotspots

Evidence for recombination between mitochondrial (mt) minichromosomes has been reported in sucking lice, but it is still not clear how frequent mt minichromosomal recombination occurs. We sequenced the mt genomes of the cattle louse Linognathus vituli and the goat louse L. africanus. Both Linognathus species have 10 mt minichromosomes, and seven of them have the same gene content and gene arrangement. Comparison of mt karyotypes revealed numerous inter-minichromosomal recombination events in the evolution of Linognathus species. Minichromosome merger, gene duplication and gene translocation occurred in the lineage leading to Linognathus lice. After the divergence of L. vituli and L. africanus, duplication, degeneration, deletion and translocation of genes also occurred independently in each species. Most of the recombination events in the Linognathus species occurred upstream of either cox3 or nad2, indicating these two locations were hotspots for inter-minichromosomal recombination. Our results provide an important perspective on mt genome evolution in metazoans.

Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae

Mitochondrial (mt) genome fragmentation has been discovered in all five parvorders of parasitic lice (Phthiraptera). To explore whether minichromosomal characters derived from mt genome fragmentation are informative for phylogenetic studies, we sequenced the mt genomes of 17 species of bird lice in Menoponidae and Laemobothriidae (Amblycera). Four species of Menoponidae (Actornithophilus sp. 1 ex [pied oystercatcher], Act. sp. 2 ex [masked lapwing], Austromenopon sp. 2 ex [sooty tern and crested tern], Myr. sp. 1 ex [satin bowerbird]) have fragmented mt genomes, whereas the other 13 species retain the single-chromosome mt genomes. The two Actornithophilus species have five and six mt minichromosomes, respectively. Aus. sp. 2 ex [sooty tern and crested tern] has two mt minichromosomes, in contrast to Aus. sp. 1 ex [sooty shearwater], which has a single mt chromosome. Myr. sp. 1 ex [satin bowerbird] has four mt minichromosomes. When mapped on the phylogeny of Menoponidae and Laemobothriidae, it is evident that mt genome fragmentation has occurred multiple times independently among Menoponidae and Laemobothriidae species. We found derived mt minichromosomal characters shared between Myrsidea species, between Actornithophilus species, and between and among different ischnoceran genera, respectively. We conclude that while mt genome fragmentation as a general feature does not unite all the parasitic lice that have this feature, each independent mt genome fragmentation event does produce minichromosomal characters that can be informative for phylogenetic studies of parasitic lice at different taxonomic levels.

A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae)

Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.

Phylogenetic Analysis of Mitochondrial Genome of Tabanidae (Diptera: Tabanidae) Reveals the Present Status of Tabanidae Classification

Simple Summary

Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. Therefore, six newly completed mitochondrial genomes of four genera of Tabanidae (Haematopota turkestanica, Chrysops vanderwulpi, Chrysops dissectus, Tabanus chrysurus, Tabanus pleskei, and Hybomitra sp. species) were sequenced and analyzed. The results show that the six newly mitochondrial genomes have quite similar structures and features. Phylogeny was inferred by analyzing the 13 amino acid sequences coded by mitochondrial genes of 22 mitogenomes (all available complete mitochondrial genomes of tabanidae). Bayesian inference, maximum likelihood trees, and maximum parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all groups, ratifies the current taxonomic classification, and provides useful genetic markers for studying the molecular ecology, systematics, and population genetics of Tabanidae.

Abstract

Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. More complete mitochondrial genomes of Tabanidae are essential for the identification and phylogeny. Therefore, this study sequenced and analyzed six complete mitochondrial (mt) genome sequences of four genera of Tabanidae for the first time. The complete mt genomes of the six new sequences are circular molecules ranging from 15,851 to 16,107 base pairs (bp) in size, with AT content ranging from 75.64 to 77.91%. The six complete mitochondrial genomes all consist of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (RRNA), 22 transfer RNA genes (tRNAs), and a control region, making a total of 37 functional subunits. ATT/ATG was the most common start codon, and the stop codon was TAA of all PCGS. All tRNA except tRNA Ser1 had a typical clover structure. Phylogeny was inferred by analyzing the 13 concatenated amino acid sequences of the 22 mt genomes. Bayesian inference, maximum-likelihood trees, and maximum-parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all genus, ratifies the current taxonomic classification, and provides effective genetic markers for molecular classification, systematics, and genetic studies of Tabanidae.

Human pediculosis, a global public health problem

Background

Human pediculosis is caused by hematophagous lice, which are transmitted between individuals via direct and/or indirect contact. Despite the public health importance of louse infestation, information concerning the global burden of pediculosis and the epidemiological landscape of louse-borne diseases is limited. The aim of this review was to summarize the biology, epidemiology, diagnosis, and control of lice infestation in humans. We also discussed the latest advances in molecular taxonomy and molecular genetics of lice.

Methods

We searched five electronic bibliographic databases (PubMed, ScienceDirect, CNKI, VIP Chinese Journal Database, and Wanfang Data) and followed a standard approach for conducting scoping reviews to identify studies on various aspects of human lice. Relevant information reported in the identified studies were collated, categorized, and summarized.

Results

A total of 282 studies were eligible for the final review. Human pediculosis remains a public health issue affecting millions of people worldwide. Emerging evidence suggests that head lice and body lice should be considered conspecific, with different genotypes and ecotypes. Phylogenetic analysis based on mitochondrial (mt) cytb gene sequences identified six distinct clades of lice worldwide. In addition to the direct effect on human health, lice can serve as vectors of disease-causing pathogens. The use of insecticides plays a crucial role in the treatment and prevention of louse infestation. Genome sequencing has advanced our knowledge of the genetic structure and evolutionary biology of human lice.

Conclusions

Human pediculosis is a public health problem affecting millions of people worldwide, particularly in developing countries. More progress can be made if emphasis is placed on the use of emerging omics technologies to elucidate the mechanisms that underpin the physiological, ecological, and evolutionary aspects of lice.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-00986-w.

Fragmented mitochondrial genomes of seal lice (family Echinophthiriidae) and gorilla louse (family Pthiridae): frequent minichromosomal splits and a host switch of lice between seals

Background

The mitochondrial (mt) genomes of 15 species of sucking lice from seven families have been studied to date. These louse species have highly dynamic, fragmented mt genomes that differ in the number of minichromosomes, the gene content, and gene order in a minichromosome between families and even between species of the same genus.

Results

In the present study, we analyzed the publicly available data to understand mt genome fragmentation in seal lice (family Echinophthiriidae) and gorilla louse, Pthirus gorillae (family Pthiridae), in particular the role of minichromosome split and minichromosome merger in the evolution of fragmented mt genomes. We show that 1) at least three ancestral mt minichromosomes of sucking lice have split in the lineage leading to seal lice, 2) one minichromosome ancestral to primate lice has split in the lineage to the gorilla louse, and 3) two ancestral minichromosomes of seal lice have merged in the lineage to the northern fur seal louse. Minichromosome split occurred 15-16 times in total in the lineages leading to species in six families of sucking lice investigated. In contrast, minichromosome merger occurred only four times in the lineages leading to species in three families of sucking lice. Further, three ancestral mt minichromosomes of sucking lice have split multiple times independently in different lineages of sucking lice. Our analyses of mt karyotypes and gene sequences also indicate the possibility of a host switch of crabeater seal louse to Weddell seals.

Conclusions

We conclude that: 1) minichromosome split contributes more than minichromosome merger in mt genome fragmentation of sucking lice, and 2) mt karyotype comparison helps understand the phylogenetic relationships between sucking louse species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08530-8.

The Complete Mitochondrial Genome of the Chicken Body Louse, Menacanthus cornutus, and Evolutionary Patterns of Extensive Gene Rearrangements in the Mitochondrial Genomes of Amblycera (Psocodea: Phthiraptera)

Animal mitochondrial (mt) genomes are typically double-strand circular DNA molecules, but diverse structural variations have been widely found in multiple groups. In parasitic lice (Phthiraptera), the structure of mt genomes varies remarkably across all five suborders. In this study, we reported the complete mt genome of a chicken body louse, Menacanthus cornutus, which has a typical single circular mt chromosome and drastic mt gene rearrangements. This mt genome is 15,693 bp in length, consisting of 13 protein-coding genes, 23 tRNA genes, 2 rRNA genes, and a control region. A comparison with a typical insect mt genome suggested that two highly similar trnM are present in the mt genome of M. cornutus. Moreover, almost every single gene was rearranged, and over half of mt genes were inverted. Phylogenetic analyses inferred from the mt genome sequences supported the monophyly and position of Amblycera. Mapped over the phylogenetic relationships of Amblycera, we identified two inversion events for the conserved gene blocks in Boopidae and Menoponidae. The inverted ND4L-ND4 was likely a synapomorphic rearrangement in Menoponidae. Our study demonstrated the importance of sequencing mt genomes for additional taxa to uncover the mechanism underlying the structural evolution of the mt genome in parasitic lice.

Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts

Insect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.

Characterization of the complete mitochondrial genomes of six horseflies (Diptera: Tabanidae)

The family Tabanidae (Insecta: Diptera) is one of the economically most important group of haematophagous insects, causing millions of livestock deaths per year. However, current knowledge on the mitochondrial genomes (mitogenomes) from this family is limited. Additional tabanid mitogenomes characterization is of utmost importance for their identification, epidemiologic and phylogenetic studies. We sequenced the mt genomes of six horseflies with an Illumina platform and their phylogenetic relationship was conducted with other infraorder Tabanomorpha members with available mt genome datasets. All six newly sequenced mitogenomes were typical 37-gene circular structures retaining the gene order of Tabanomorpha. The trnQ, trnM and trnA were highly conserved among the six mitogenomes (identity = 100%). The TΨC arm and variable loop regions were relatively more variable compared to the amino acid receptor arm, anticodon arm and DHU arm of the tRNAs. Among 13 protein-coding genes (PCGs) of tabanids mitogenomes, the highest nucleotide diversity was detected in atp8, cox1, cox3, nad6 and cytb (0.1 for each). In addition, atp8 genes exhibited the highest evolutionary rate (ω = 0.24) among 13 PCGs. The interspecies K2P genetic distances among some Tabanus spp. across the mitogenome was greater (0.08) than intergeneric genetic distance between T. amaenus and Atylotus miser (0.07). Phylogenetic analyses revealed non-monophyletic relationships among horseflies of the genus Tabanus. The present study showed mt gene order is highly conserved within Tabanus species. Our mito-phylogenomic analysis supports the paraphyly of the genus Tabanus. The new data provide novel genetic markers for studies of population genetics and systematics of horseflies.

Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

Background

The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes.

Results

We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes.

Conclusions

We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07859-w.

The complete mitochondrial genome of capillariid nematodes (Eucoleus annulatus): A novel gene arrangement and phylogenetic implications

Capillariid nematode is a group of endoparasites of vertebrates with a complex taxonomy, causing significant economic losses to poultry industry. The taxonomic status of the genus Eucoleus remained controversial for several decades. Mitochondrial (mt) DNA provides useful genetic markers for accurate identification of species, but complete mt genome sequences have been lacking for any Capillariid nematodes. In the present study, we decoded the complete mt genome of E. annulatus and examined its phylogenetic relationship with selected members of the class Enoplea nematodes. The circular mt genome of E. annulatus was 14,118 bp, encoded 37 genes with a single non-coding region and showed substantial gene rearrangements (especially tRNA genes) compared to other nematodes studied to date. The complete mt genome of E. annulatus showed a clear A + T bias in nucleotide composition. The number of A (5404) was approximately equal to T (5405) and the GC-skew was negative on average (-0.073). Phylogenetic analyses based on 18S rDNA placed Eucoleus spp. well apart from each other and supported the proposal that Eucoleus and Capillaria are two distinct genera. Similarly, Bayesian inference (BI) and Maximum likelihood (ML) phylogenies based on mtDNA sequences revealed that the family Capillariidae is more closely related to the family Trichuridae than to the family Trichinellidae. This is the first report of the complete mt genome of capillariid nematodes, and it will provide additional genetic markers for studying the molecular epidemiology, population genetics and systematics of capillariid nematodes and should have implications for the molecular diagnosis, prevention, and control of capillariosis in animals.

Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles

Background

Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera.

Methods

Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods.

Results

The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100).

Conclusions

These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04776-5.

The complete mitochondrial genome sequences of the cat flea Ctenocephalides felis felis (Siphonaptera: Pulicidae) support the hypothesis that C. felis isolates from China and USA were the same C. f. felis subspecies

The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the most important ectoparasite in cats and dogs worldwide. Over the years, there has been much dispute regarding the taxonomic and systematic status of C. felis. Mitochondrial (mt) genome sequences are useful genetic markers for the identification and differentiation of ectoparasites, but the mt genome of C. felis and its subspecies has not yet been entirely characterized. In the present study, the entire mt genome of C. f. felis from China was sequenced and compared with that of C. felis from the USA. Both contain 37 genes and a long non-coding region of >6 kbp. The molecular identity between the Chinese and American isolates was 99%, except for the non-coding region. The protein-coding genes showed differences at both the nucleotide (1.2%) and amino acid (1%) levels. Interestingly, the cox1 gene of the Chinese isolate had an unusual putative start codon (TTT). Taken together, our analyses strongly support the hypothesis that C. felis isolates from China and the USA were the same C. f. felis subspecies. The mt genome sequence of the C. f. felis China isolate presented in this study provides useful molecular markers to further address the taxonomy and systematics of C. felis.