Fragments Of Mitochondrial Genome Research Articles

Microscale total genomic DNA was used to explore the complete mitochondrial genomes of two biting midge species of the family Ceratopogonidae (Insecta: Diptera)

BackgroundBiting midges (Ceratopogonidae, Diptera) are small insects, with body sizes ranging from 1–5 mm, and the family included 6,276 extant and 303 fossil species in 2022. But only a few mitochondrial genomes of Ceratopogonidae species have been reported, and those from several species have not been amplified. Sequencing of total or mitochondrial genomic DNA requires large amounts insect samples; however, obtaining these samples is very difficult for some insect species. The complete mitochondrial genome sequences of some insect species were cloned by long PCR, but degenerate or multiple pairs of primers were needed; thus, the long PCR method was optimized and improved in this study. The optimized method was named the two-fragment cloning method. In this study, we sequenced and analysed the complete mitochondrial genomes of two biting midge species, Forcipomyia (Lasiohelea) humilavolita (16,885 bp) and Dasyhelea bilineata (16,189 bp), via the two-fragment cloning method following the sequencing of PCR products.ResultsThe two mitochondrial genome fragments of F. humilavolita and D. bilineata were successfully cloned by using the two-fragment cloning method with only single-round PCR and the nested PCR method with two-round PCR, respectively. F. humilavolita and D. bilineata showed highly conserved mitogenomes, with similar gene orders, 37 typical genes and a noncoding A + T-rich region. The nucleotide composition of these genomes was highly biased towards A + T nucleotides (78.15% and 78.25%), and the AT skews (-0.001894 and 0.011999), negative GC skews (-0.535714 and -0.217391), and codon usage were determined. All 22 tRNA genes presented typical cloverleaf secondary structures, except for trnS1-NCU, which lacked the dihydrouridine arm. Phylogenetic analyses of the PCGAA and PCG123RNA datasets revealed that F. humilavolita and D. bilineata were grouped together on the same branch as the other Ceratopogonidae species were F. makanensis, F. pulchrithorax, Culicoides arakawae and C. brevitarsis.ConclusionDifferent PCG genes were terminated with an incomplete T residue and AT skews in F. humilavolita and D. bilineata. Whether these differences occur between species or genera requires study of the complete mitochondrial genomes of more species of Ceratopogonidae, and the two-fragment cloning method can be used for this. In the key first step, the universal primers for cloning COX1 and 16S rRNA from insects are used, so the two-fragment cloning method may be widely used for insects.

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.

Codon Usage Characteristics and Evolutionary Analysis of Mitochondrial Genome of Winter Squash (Cucurbita maxima Duch.)

Mitochondrial genomes are essential components of eukaryotic cells, understanding their structural characteristics and codon usage bias is critical. Winter squash (Cucurbita maxima Duch ex Poiret) is an economically important cucurbit crop. To clarify its structural characteristics and codon usage bias of mitochondrial genome, as well as the evolutionary characteristics in the Cucurbitaceae family, whole genome sequencing analysis of C. maxima mitochondrial genome was carried out. The results revealed that the total length of the C. maxima mitochondrial genome was 640,814 bp, containing 9,162,318,300 bp of bases. There were 68 annotated genes identified. The mitochondrial coding genes of C. maxima exhibited an average GCall content of 42.57%, with the last position enriched in A/T bases. Codon usage analysis indicated weak codon bias, with the effective codon number (ENC) ranging from 44.22 to 61.00. Correlation analysis and neutrality plot analysis demonstrated a nonsignificant correlation between GC3 and GC12. PR2-plot and ENC-plot analysis further supported the influence of natural selection on the codon preference in the C. maxima mitochondrial genome. Relative synonymous codon usage (RSCU) analysis identified 19 optimal codons, with a preference for U or A as the final base. The analysis of scattered repeat sequences in the genome indicated a high frequency of forward and palindromic repeats in the C. maxima mitochondrial genome. Nucleic acid diversity analysis highlighted rpl5 as the gene with the highest variability. Comparative analysis of mitochondrial structure and phylogenetic tree analysis revealed a close evolutionary relationship between C. maxima and Cucurbita pepo, showing synteny in evolution. Homologous fragment analysis demonstrated a similarity of over 70% between the C. maxima mitochondrial genome and chloroplast genome fragments. These findings provide a foundation for C. maxima identification and phylogenetic studies.

Morphological characteristics and genetic diversity of floating and attached Ulva prolifera––A case study in the Yellow Sea, China

Green tides in the Yellow Sea have occurred periodically since 2007, impacting the ecological environment and green algal communities along the coasts of Jiangsu and Shandong provinces in China. To investigate the morphological characteristics and genetic diversity of Ulva prolifera, we conducted surveys and comparative analyses of both its floating and attached forms along the coastal areas of Jiangsu and Shandong. The results revealed that the external morphology of the floating U. prolifera was multibranched. The attached U. prolifera displayed significant morphological variation among individuals. Based on the analysis of the amplified characteristic bands of the chloroplast gene, it was shown that both floating and attached U. prolifera could hybridize with Ulva linza. The genetic diversity of U. prolifera was studied using mitochondrial and chloroplast genome fragments. All floating U. prolifera and three strains of attached U. prolifera belonged to the same haplotype. The genetic diversity of floating U. prolifera was low, and there were some genetic differences with attached U. prolifera. The attached U. prolifera displayed a higher level of genetic diversity with abundant sites of variation and haplotypes.

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes.

The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.

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.

DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands.

Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.

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

BackgroundThe 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.ResultsIn 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.ConclusionsWe 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.

Comparative analyses of the fragmented mitochondrial genomes of wild pig louse Haematopinus apri from China and Japan.

The wild pig louse Haematopinus apri is one of the commonest ectoparasites of wild pigs. In the present study, the entire mitochondrial (mt) genome of wild pig louse H. apri from China was sequenced and compared with previously characterized wild pig louse H. apri from Japan. We identified all of the 37 mt genes in the wild pig louse H. apri from China which are on nine circular minichromosomes. Each mt minichromosome is 2.9 kb–4.2 kb size and contains 2–8 genes and one non-coding region (1543 bp-2534 bp). The number of minichromosomes, gene content and gene order in the both mt genomes of wild pig louse H. apri from China and Japan are the same. The identity of the both mt genomes (except for non-coding regions) was 98.3% between wild pig louse H. apri from China and Japan. The entire mt genome sequence (except for non-coding regions) of wild pig louse H. apri from China is longer (3 bp) than that from Japan. For the 13 protein-coding genes, this comparison showed sequence differences in each gene at both the nucleotide (0.8%–2.4%) and amino acid (0.4%–3.5%) levels. The most conserved of these genes was the nad6, whereas the nad2 was least conserved at the nucleotide levels. This is the first comprehensive comparison of the mt genomes of a louse species from different geographic locations. This useful data provides additional genetic markers to study the phylogeny, systematics and population genetics of wild pig louse H. apri.

Fragmentation in mitochondrial genomes in relation to elevated sequence divergence and extreme rearrangements

BackgroundA single circular mitochondrial (mt) genome is a common feature across most metazoans. The mt-genome includes protein-coding genes involved in oxidative phosphorylation, as well as RNAs necessary for translation of mt-RNAs, whose order and number are highly conserved across animal clades, with few known exceptions of alternative mt-gene order or mt-genome architectures. One such exception consists of the fragmented mitochondrial genome, a type of genome architecture where mt-genes are split across two or more mt-chromosomes. However, the origins of mt-genome fragmentation and its effects on mt-genome evolution are unknown. Here, we investigate these origin and potential mechanisms underlying mt-genome fragmentation, focusing on a genus of booklice, Liposcelis, which exhibits elevated sequence divergence, frequent rearrangement of mt-gene order, and fragmentation of the mt genome, and compare them to other Metazoan clades.ResultsWe found this genus Liposcelis exhibits very low conservation of mt-gene order across species, relative to other metazoans. Levels of gene order rearrangement were, however, unrelated to whether or not mt-genomes were fragmented or intact, suggesting mitochondrial genome fragmentation is not affecting mt-gene order directly. We further investigated possible mechanisms underpinning these patterns and revealed very high conservation of non-coding sequences at the edges of multiple recombination regions across populations of one particular Liposcelis species, supportive of a hypothesis that mt-fragmentation arises from recombination errors between mt-genome copies. We propose these errors may arise as a consequence of a heightened mutation rate in clades exhibiting mt-fragmentation. Consistent with this, we observed a striking pattern across three Metazoan phyla (Arthropoda, Nematoda, Cnidaria) characterised by members exhibiting high levels of mt-gene order rearrangement and cases of mt-fragmentation, whereby the mt-genomes of species more closely related to species with fragmented mt-genomes diverge more rapidly despite experiencing strong purifying selection.ConclusionsWe showed that contrary to expectations, mt-genome fragmentation is not correlated with the increase in mt-genome rearrangements. Furthermore, we present evidence that fragmentation of the mt-genome may be part of a general relaxation of a natural selection on the mt-genome, thus providing new insights into the origins of mt-genome fragmentation and evolution.

Interactions between mitochondrial and nuclear genomes and co-regulation of mitochondrial and nuclear gene expression in reciprocal intergeneric hybrids between Carassius auratus red var. × Cyprinus carpio L.

Genetic interactions between nuclear and mitochondrial genomes always play an important role in growth and development. However, it is not feasible to directly perform these studies in some animals. The reciprocal hybrid fishes obtained from intergeneric hybridization are an effective research model for the same nuclear genome and different mitochondrial genomes. The transcriptomes of embryonic development (Blastula Period, Gastrula Period, Segmentation Period and Hatching Period) were obtained from the two reciprocal hybrids of Carassius auratus red var. (RCC) ​× ​ Cyprinus carpio L. (CC) and their parents. Most of the reads (average ​> ​99.90%) in the transcriptome of F 1 -RC ( C. auratus red var. (♀) ​× ​ C. carpio L. (♂)) and F 1 -CR ( C. carpio L. (♀) ​× ​ C. auratus red var. (♂)) were optimally mapped to the maternal mitochondrial genome (MMG), respectively. Then, the other reads with optimally mapped to paternal mitochondrial genome exhibited that the partial coverages and low-level (<0.4%) expressions of paternal mitochondrial genes were in the four developmental stages of them, especially hatching period, in which paternal mitochondrial DNA (mtDNA) is always eliminated in animals. In the four stages, some changes of 13 mitochondrial gene expressions were occurred in comparisons of the female parents and their hybrid progenies (F 1 -RC vs. RCC and F 1 -CR vs. CC), although no significantly differential expression (DE) was detected in them. Moreover, in each embryonic development stages, the positive correlation between the number of differential expression of nuclear-encoded mitochondrial genes and the p-value of differential expression of mitochondrial genes help us understanding how the detail of mitochondrial-nuclear genetic interactions operate in hybrids. The detection of paternal mitochondrial genome fragments in hatching period provides us insight into potential escape mechanisms which may disrupt or inactivate PME in hybrids. These differential expression of nuclear-encoded mitochondrial genes between reciprocal hybrids may help us understanding of the genetic basis of growth in hybrids and used in their breeding project.

Mitochondrial genomes within bark lice (Insecta: Psocodea: Psocomorpha) reveal novel gene rearrangements containing phylogenetic signal

ABSTRACTPsocodea (booklice and parasitic lice) is an order of insects containing species with extensive mitochondrial genome rearrangements, particularly within the suborder Troctomorpha, in which some species possess an extremely fragmented mitochondrial genome with several small minichromosomes. In the remaining suborders of Psocodea, there are groups with the ancestral pancrustacean arrangement, quite extensive rearrangements (e.g. Trogiomorpha), or in which the small number of species analysed to date have rearrangements of only a few protein‐coding genes and/or tRNAs (e.g. Psocomorpha). Despite the apparent high rate of rearrangements in the order as a whole, a small number of complete mitochondrial genomes are available, especially for suborder Psocomorpha, the largest free‐living suborder. To understand the evolution of the gene arrangement of the mitochondrial genome within Psocomorpha and its phylogenetic implications, we assembled and analysed the mitochondrial genomes of 33 species of bark lice belonging to nine families in two infraorders. Within the infraorder Homilopsocidea, four families were analysed, mainly from Lachesillidae (which included 22 species of this family). Within the infraorder Caeciliusetae, seven species representing five families were analysed. Mitochondrial gene rearrangements were identified in seven of the nine families. Some of these rearrangements were unique to a single species, while some contained phylogenetic signal, being shared by related species. These rearrangements typically corresponded to transpositions and inversions of tRNAs, possibly caused by tandem duplication–random loss (TDRL) and/or recombination events. Phylogenetic analyses of mitochondrial gene sequences provided phylogenetic resolution for several branches of the tree, including monophyly of Lachesillinae. The genus Hemicaecilius Enderlein was found to be embedded within the genus Lachesilla Westwood, rending the latter paraphyletic. Monophyly was also never recovered for Lachesillidae and Elipsocidae as currently defined. However, instability was observed for some higher level relationships within Psocomorpha, including the relationships among the major clades of Lachesillidae.

A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia.

Mitochondrial genome content and structure vary widely across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial genome sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented cytochrome genes in Toxoplasma and related tissue coccidia and evolution of a novel genome architecture consisting minimally of 21 sequence blocks (SBs) totaling 5.9 kb that exist as nonrandom concatemers. Single-molecule Nanopore reads consisting entirely of SBs ranging from 0.1 to 23.6 kb reveal both whole and fragmented cytochrome genes. Full-length cytochrome transcripts including a divergent coxIII are detected. The topology of the mitochondrial genome remains an enigma. Analysis of a cob point mutation reveals that homoplasmy of SBs is maintained. Tissue coccidia are important pathogens of man and animals, and the mitochondrion represents an important therapeutic target. The mtDNA sequence has been elucidated, but a definitive genome architecture remains elusive.

Генотипирование черноморских трематод семейства Opecoelidae по митохондриальным маркерам

Opecoelidae Ozaki, 1925 (Trematoda: Opecoeloidea) — ведущее по числу видов и родов семейство трематод в Чёрном море. Мариты наиболее распространённых видов черноморских опецелидных трематод подробно описаны морфологически, однако сведения о структуре их геномов отрывочны, а данные о митохондриальных геномах отсутствуют полностью. Цель исследования — получить первые сведения о строении участков митохондриального генома представителей наиболее распространённых в Чёрном море в современный период родов трематод семейства Opecoelidae для последующего уточнения их таксономического статуса. Филогенетические отношения внутри анализируемой части этого семейства реконструированы на основе данных, полученных нами, и соответствующих данных из GenBank с помощью алгоритма Maximum Likelihood и модели нуклеотидных замен HKY. Для укоренения филогенетического дерева использованы соответствующие последовательности Brachycladium goliath (Brachycladioidea: Brachycladiidae). Поскольку последовательности CO1 — стандартного и наиболее популярного митохондриального маркера — для исследуемых родов опецелид до сих пор не были известны, нами на основе известных соответствующих последовательностей Xiphidiata разработаны праймеры для амплификации фрагмента CO1, чтобы впервые провести соответствующий филогенетический анализ. Впервые определены и депонированы в GenBank нуклеотидные последовательности фрагментов митохондриальных генов CO1 и 16S черноморских трематод Cainocreadium flesi Korniychuk &amp; Gaevskaya, 2000, Gaevskajatrema perezi (Mathias, 1926) Gibson &amp; Bray, 1982 и Helicometra fasciata (Rudolphi, 1819) Odhner, 1902 от разных видов дефинитивных хозяев — рыб. У C. flesi не выявлено специфичных к окончательным хозяевам — рыбам линий по структуре фрагмента митохондриального гена CO1, однако отмечено высокое CO1-нуклеотидное разнообразие. У марит черноморских H. fasciata определена приуроченная к зеленушкам-руленам Symphodus tinca CO1-гаплогруппа, статус которой требует дальнейшего выяснения; необходимы экологические и генетические исследования предполагаемого видового комплекса H. fasciata из разных акваторий. При анализе последовательностей фрагмента митохондриального гена 16S рРНК гостальных генетических линий у H. fasciata выделить не удалось. У черноморских G. perezi не обнаружено значительных различий по фрагменту 16S между трематодами из окончательных хозяев разных видов, однако внутривидовое 16S-нуклеотидное разнообразие оказалось высоким.

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

BackgroundThe 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.MethodsWe 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.ResultsFragmented 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.ConclusionsComparison 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.

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.

Phylogeny of certain members of Hyrcanus group (Diptera: Culicidae) in China based on mitochondrial genome fragments

BackgroundSpecies of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear.MethodsFive members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood.FindingsFour parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)).ConclusionsThe An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.

The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.

Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes.

Although mitochondrial genomes are typically thought of as single circular molecules, these genomes are fragmented into multiple chromosomes in many eukaryotes, raising intriguing questions about inheritance and (in)stability of mtDNA in such systems. A previous comparison of mitochondrial genomes from two different individuals of the angiosperm species Silene noctiflora found variation in the presence of entire mitochondrial chromosomes. Here, we expand on this work with a geographically diverse sampling of 25 S. noctiflora populations and the closely related species S. turkestanica and S. undulata. Using a combination of deep sequencing and PCR-based screening for the presence of 22 different mitochondrial chromosomes, we found extensive variation in the complement of chromosomes across individuals. Much of this variation could be attributed to recent chromosome loss events, suggesting that the massively expanded and fragmented mitochondrial genomes of S. noctiflora may have entered a phase of genome reduction in which they are losing entire chromosomes at a rapid rate. Sequence analysis of mitochondrial and plastid genomes revealed genealogical differences both between these organelles and within the mitochondrial genome, indicating a history of recombination. Evidence that recombination has generated novel combinations of alleles was more frequent between loci on different mitochondrial chromosomes than it was within chromosomes. Therefore, the fragmentation of mitochondrial genomes and the assortment of chromosomes during mitochondrial inheritance appears to have contributed to a history of sexual-like recombination in the mtDNA of this species.