Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta)

Drastic variation in mitochondrial genome organization between two congeneric species of bird lice (Philopteridae: Ibidoecus)

The over 4,100 species of bird lice are classified into 214 genera in the parvorders Amblycera and Ischnocera. Congeneric species of bird lice usually share much similarity in morphology and in mitochondrial (mt) genome organization. Two recent studies, however, reported substantial intra-genus variation in mt genome organization in bird lice. Both the ancestral single-chromosome mt genome and a fragmented mt genome with two or three minichromosomes were observed in the genera Austromenopon and Laemobothrion. To better understand intra-genus variation in mt genome organization, we sequenced the complete mt genome of the white spoonbill louse Ibidoecus plataleae and compared it with that of the glossy ibis feather louse Ibidoecus bisignatus reported previously. We found that I. plataleae had a fragmented mt genome with 12 minichromosomes; each minichromosome was 2,798 to 3,628 bp in size and had 2 to 6 genes. This is in stark contrast to the mt genome of I. bisignatus, which has all genes on a single chromosome, 14,909 bp in size. This is the most drastic intra-genus variation in mt genome organization observed to date in animals, indicating an unprecedented rapid process of mt genome fragmentation in the genus Ibidoecus. The divergence time between I. plataleae and I. bisignatus is currently unknown but is estimated to be less than 23 million years. Either many minichromosal split events occurred after I. plataleae diverged from I. bisignatus, or one minichromosome splits into multiple minichromosomes in a single event. Sequencing and comparing more Ibidoecusi species will help understand the unusual mt genome fragmentation in this genus.

Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution

While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.

Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species

The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.

Complete mitochondrial genome of Stethoconus japonicus (Hemiptera: Miridae): Insights into the evolutionary traits within the family Miridae

The mitochondrial (mt) genome sequence of insects possesses numerous evolutionary traits. To better understand the evolution of mt genomes within the family Miridae, the complete mt genome of the predatory Japanese plant bug Stethoconus japonicus Schumacher was sequenced before undertaking a comparative analysis of all reported plant bug mt genomes. The mt genome of S. japonicus is a closed-circular and double-stranded DNA molecule of 16,274 bp (GenBank: MK341530), which consists of 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and a putative control region (CR). Consistent with other plant bugs, the mt genome of S. japonicus is strongly AT-biased (73.49 %) with A-skewed (0.202) and C-skewed (-0.248). All 13 PCGs initiate translation using ATN codons and TAA served as complete stop codons for eight PCGs, which as incomplete stop codon "T-" for cox1, nad1, nad5-6 and "TA-" for cox2. Regarding other features, all 22 tRNAs could be folded into typical cloverleaf secondary structures. The control region is 1,717 bp and contains a long tandem repeat sequence of a 165 bp unit repeated six times. Similar sequence with variable number of tandemly repeated units from intra-genus CRs is a distinct characteristic of plant bug mt genomes. Phylogenetic relationships of 15 bugs were eventually analyzed based on Maximum likelihood (ML) and Bayesian inference (BI) methods using 17 mt genome sequences. In the phylogenetic trees, species from a same genus or subfamily are clustered into a branch with high supporting values.and the result suggest that Deraeocorinae is more closely related to Mirinae than Bryocorinae. Finally, this study revealed that mutation of tRNA anticodon is a useful phylogenetic marker that could be of significance for studies of evolutionary patterns.

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.

Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice

Simple Summary

New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales.

Abstract

Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.

Independent evolution of highly variable, fragmented mitogenomes of parasitic lice

The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.

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.

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.

Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse

Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average of 26% of each chromosome was composed of non-gene sequences. Within the non-gene region of each chromosome, there was a 79-nt nucleotide sequence that was identical among chromosomes and a conserved sequence with secondary structure that was always followed by a poly-T region. We hypothesize that these regions may be important in the initiation of transcription and DNA replication, respectively. The G. aurei genome shares 8 derived gene clusters with other chewing lice of mammals, but in G. aurei, genes on several chromosomes are not contiguous.

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.

Identification of Lice Stored in Alcohol Using MALDI-TOF MS

Lice pose major public and veterinary health problems with economic consequences. Their identification is essential and requires the development of an innovative strategy. MALDI-TOF MS has recently been proposed as a quick, inexpensive, and accurate tool for the identification of arthropods. Alcohol is one of the most frequently used storage methods and makes it possible to store samples for long periods at room temperature. Several recent studies have reported that alcohol alters protein profiles resulting from MS analysis. After preliminary studies on frozen lice, the purpose of this research was to evaluate the influence of alcohol preservation on the accuracy of lice identification by MALDI-TOF MS. To this end, lice stored in alcohol for variable periods were submitted for MS analysis and sample preparation protocols were optimized. The reproducibility and specificity of the MS spectra obtained on both these arthropod families allowed us to implement the reference MS spectra database (DB) with protein profiles of seven lice species stored in alcohol. Blind tests revealed a correct identification of 93.9% of Pediculus humanus corporis (Linnaeus, 1758) and 98.4% of the other lice species collected in the field. This study demonstrated that MALDI-TOF MS could be successfully used for the identification of lice stored in alcohol for different lengths of time.

HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades

Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.

Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera

Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.

Variation of mitochondrial minichromosome composition in Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats

Background

The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice (Hoplopleura kitti and H. akanezumi) from this family, but some minichromosomes were unidentified in their mt genomes.

Methods

We sequenced the mt genome of the rat louse Hoplopleura sp. with an Illumina platform and compared its mt genome organization with H. kitti and H. akanezumi.

Results

Fragmented mt genome of the rat louse Hoplopleura sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8–2.7 kb long and contains 1–5 genes and one large non-coding region. The gene content and arrangement of mt minichromosomes of Hoplopleura sp. (n = 3) and H. kitti (n = 3) are different from those in H. akanezumi (n = 3). Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the Hoplopleura sp. was more closely related to H. akanezumi than to H. kitti, and then they formed a monophyletic group.

Conclusions

Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus Hoplopleura. Hoplopleura sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provide useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

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

We report for the first time the fragmented mitochondrial (mt) genomes of two Pedicinus species: Pedicinus obtusus and Pedicinus badii, and compared them with the lice of humans and chimpanzees. Despite being congeneric, the two monkey lice are distinct from each other in mt karyotype. The variation in mt karyotype between the two Pedicinus lice is the most pronounced among the congeneric species of sucking lice observed to date and is attributable to the opposite directions between them in mt karyotype evolution. Two of the inferred ancestral mt minichromosomes of the higher primate lice merged as one in the macaque louse whereas one of the ancestral minichromosomes split into two in the colobus louse after these two species diverged from their most recent common ancestor. Our results showed that mt genome fragmentation was a two-way process in the higher primate lice, and minichromosome merger was more common than previously thought.

Development of MALDI-TOF mass spectrometry for the identification of lice isolated from farm animals

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used for the rapid identification of microorganisms isolated from clinical samples and has been recently successfully applied to the identification of arthropods. In the present study, this proteomics tool was used to identify lice collected from livestock and poultry in Algeria. The MALDI-TOF MS spectra of 408 adult specimens were measured for 14 species, including Bovicola bovis, B. ovis, B. caprae, Haematopinus eurysternus, Linognathus africanus, L. vituli, Solenopotes capillatus, Menacanthus stramineus, Menopon gallinae, Chelopistes meleagridis, Goniocotes gallinae, Goniodes gigas, Lipeurus caponis and laboratory reared Pediculus humanus corporis. Good quality spectra were obtained for 305 samples. Spectral analysis revealed intra-species reproducibility and inter-species specificity that were consistent with the morphological classification. A blind test of 248 specimens was performed against the in-lab database upgraded with new spectra and validated using molecular tools. With identification percentages ranging from 76% to 100% alongside high identification scores (mean = 2.115), this study proposes MALDI-TOF MS as an effective tool for discriminating lice species.

Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication-random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.

Mitochondrial Genome Fragmentation Unites the Parasitic Lice of Eutherian Mammals

Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the controversial suborder-level phylogeny of parasitic lice (order Phthiraptera). There are approximately 5000 species of parasitic lice in four suborders (Amblycera, Ischnocera, Rhynchophthirina, and Anoplura), which infest mammals and birds. The phylogenetic relationships among these suborders are unresolved despite decades of studies. We sequenced the mt genomes of eight species of parasitic lice and compared them with 17 other species of parasitic lice sequenced previously. We found that the typical single-chromosome mt genome is retained in the lice of birds but fragmented into many minichromosomes in the lice of eutherian mammals. The shared derived feature of mt genome fragmentation unites the eutherian mammal lice of Ischnocera (family Trichodectidae) with Anoplura and Rhynchophthirina to the exclusion of the bird lice of Ischnocera (family Philopteridae). The novel clade, namely Mitodivisia, is also supported by phylogenetic analysis of mt genome and cox1 gene sequences. Our results demonstrate, for the first time, that organelle genome fragmentation is informative for resolving controversial high-level phylogenies.

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

The Mitochondrial Genome of the Guanaco Louse, Microthoracius praelongiceps: Insights into the Ancestral Mitochondrial Karyotype of Sucking Lice (Anoplura, Insecta)

Fragmented mitochondrial (mt) genomes have been reported in 11 species of sucking lice (suborder Anoplura) that infest humans, chimpanzees, pigs, horses, and rodents. There is substantial variation among these lice in mt karyotype: the number of minichromosomes of a species ranges from 9 to 20; the number of genes in a minichromosome ranges from 1 to 8; gene arrangement in a minichromosome differs between species, even in the same genus. We sequenced the mt genome of the guanaco louse, Microthoracius praelongiceps, to help establish the ancestral mt karyotype for sucking lice and understand how fragmented mt genomes evolved. The guanaco louse has 12 mt minichromosomes; each minichromosome has 2-5 genes and a non-coding region. The guanaco louse shares many features with rodent lice in mt karyotype, more than with other sucking lice. The guanaco louse, however, is more closely related phylogenetically to human lice, chimpanzee lice, pig lice, and horse lice than to rodent lice. By parsimony analysis of shared features in mt karyotype, we infer that the most recent common ancestor of sucking lice, which lived ∼75 Ma, had 11 minichromosomes; each minichromosome had 1-6 genes and a non-coding region. As sucking lice diverged, split of mt minichromosomes occurred many times in the lineages leading to the lice of humans, chimpanzees, and rodents whereas merger of minichromosomes occurred in the lineage leading to the lice of pigs and horses. Together, splits and mergers of minichromosomes created a very complex and dynamic mt genome organization in the sucking lice.

The Highly Divergent Mitochondrial Genomes Indicate That the Booklouse, Liposcelis bostrychophila (Psocoptera: Liposcelididae) Is a Cryptic Species

The booklouse, Liposcelis bostrychophila is an important storage pest worldwide. The mitochondrial (mt) genome of an asexual strain (Beibei, China) of the L. bostrychophila comprises two chromosomes; each chromosome contains approximate half of the 37 genes typically found in bilateral animals. The mt genomes of two sexual strains of L. bostrychophila, however, comprise five and seven chromosomes, respectively; each chromosome contains one to six genes. To understand mt genome evolution in L. bostrychophila, and whether L. bostrychophila is a cryptic species, we sequenced the mt genomes of six strains of asexual L. bostrychophila collected from different locations in China, Croatia, and the United States. The mt genomes of all six asexual strains of L. bostrychophila have two chromosomes. Phylogenetic analysis of mt genome sequences divided nine strains of L. bostrychophila into four groups. Each group has a distinct mt genome organization and substantial sequence divergence (48.7–87.4%) from other groups. Furthermore, the seven asexual strains of L. bostrychophila, including the published Beibei strain, are more closely related to two other species of booklice, L. paeta and L. sculptilimacula, than to the sexual strains of L. bostrychophila. Our results revealed highly divergent mt genomes in the booklouse, L. bostrychophila, and indicate that L. bostrychophila is a cryptic species.

Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus

We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.

The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae

There are numerous gene rearrangements and transfer RNA gene absences existing in mitochondrial (mt) genomes of Aleyrodidae species. To understand how mt genomes evolved in the family Aleyrodidae, we have sequenced the complete mt genome of Aleurocanthus camelliae and comparatively analyzed all reported whitefly mt genomes. The mt genome of A. camelliae is 15,188 bp long, and consists of 13 protein-coding genes, two rRNA genes, 21 tRNA genes and a putative control region (GenBank: KU761949). The tRNA gene, trnI, has not been observed in this genome. The mt genome has a unique gene order and shares most gene boundaries with Tetraleurodes acaciae. Nineteen of 21 tRNA genes have the conventional cloverleaf shaped secondary structure and two (trnS₁ and trnS₂) lack the dihydrouridine (DHU) arm. Using ARWEN and homologous sequence alignment, we have identified five tRNA genes and revised the annotation for three whitefly mt genomes. This result suggests that most absent genes exist in the genomes and have not been identified, due to be lack of technology and inference sequence. The phylogenetic relationships among 11 whiteflies and Drosophila melanogaster were inferred by maximum likelihood and Bayesian inference methods. Aleurocanthus camelliae and T. acaciae form a sister group, and all three Bemisia tabaci and two Bemisia afer strains gather together. These results are identical to the relationships inferred from gene order. We inferred that gene rearrangement plays an important role in the mt genome evolved from whiteflies.

The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers

Background

The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to this conserved structure, such as the division of the genome into multiple chromosomes, have been reported in a diverse set of metazoans. We report on the two circle multipartite mt genome of a newly described cyst nematode, Globodera ellingtonae.

Results

The G. ellingtonae mt genome was found to be comprised of two circles, each larger than any other multipartite circular mt chromosome yet reported, and both were larger than the single mt circle of the model nematode Caenorhabditis elegans. The genetic content of the genome was disproportionately divided between the two circles, although they shared a ~6.5 kb non-coding region. The 17.8 kb circle (mtDNA-I) contained ten protein-coding genes and two tRNA genes, whereas the 14.4 kb circle (mtDNA-II) contained two protein-coding genes, 20 tRNA genes and both rRNA genes. Perhaps correlated with this division of genetic content, the copy number of mtDNA-II was more than four-fold that of mtDNA-I in individual nematodes. The difference in copy number increased between second-stage and fourth-stage juveniles.

Conclusions

The segregation of gene types to different mt circles in G. ellingtonae could provide benefit by localizing gene functional types to independent transcriptional units. This is the first report of both two-circle and several-circle mt genomes within a single genus. The differential copy number associated with this multipartite mt organization could provide a model system for deconstructing mechanisms regulating mtDNA copy number both in somatic cells and during germline development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3047-x) contains supplementary material, which is available to authorized users.

The Mitochondrial Cytochrome Oxidase Subunit I Gene Occurs on a Minichromosome with Extensive Heteroplasmy in Two Species of Chewing Lice, Geomydoecus aurei and Thomomydoecus minor

In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two species of chewing lice found on pocket gophers, Geomydoecus aurei and Thomomydoecus minor, are fragmented with the 1,536 base-pair (bp) cytochrome-oxidase subunit I (cox1) gene occurring as the only protein-coding gene on a 1,916-1,964 bp minicircular chromosome in the two species, respectively. The cox1 gene of T. minor begins with an atypical start codon, while that of G. aurei does not. Components of the non-protein coding sequence of G. aurei and T. minor include a tRNA (isoleucine) gene, inverted repeat sequences consistent with origins of replication, and an additional non-coding region that is smaller than the non-coding sequence of other lice with such fragmented mitochondrial genomes. Sequences of cox1 minichromosome clones for each species reveal extensive length and sequence heteroplasmy in both coding and noncoding regions. The highly variable non-gene regions of G. aurei and T. minor have little sequence similarity with one another except for a 19-bp region of phylogenetically conserved sequence with unknown function.

The mitochondrial genome of booklouse, Liposcelis sculptilis (Psocoptera: Liposcelididae) and the evolutionary timescale of Liposcelis

Bilateral animals are featured by an extremely compact mitochondrial (mt) genome with 37 genes on a single circular chromosome. To date, the complete mt genome has only been determined for four species of Liposcelis, a genus with economic importance, including L. entomophila, L. decolor, L. bostrychophila, and L. paeta. They belong to A, B, or D group of Liposcelis, respectively. Unlike most bilateral animals, L. bostrychophila, L. entomophila and L. paeta have a bitipartite mt genome with genes on two chromosomes. However, the mt genome of L. decolor has the typical mt chromosome of bilateral animals. Here, we sequenced the mt genome of L. sculptilis, and identified 35 genes, which were on a single chromosome. The mt genome fragmentation is not shared by the D group of Liposcelis and the single chromosome of L. sculptilis differed from those of booklice known in gene content and gene arrangement. We inferred that different evolutionary patterns and rate existed in Liposcelis. Further, we reconstructed the evolutionary history of 21 psocodean taxa with phylogenetic analyses, which suggested that Liposcelididae and Phthiraptera have evolved 134 Ma and the sucking lice diversified in the Late Cretaceous.