The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA.

The mammalian mitochondrial transcription termination factor mTERF binds with high affinity to a site within the tRNA(Leu(UUR)) gene and regulates the amount of read through transcription from the ribosomal DNA into the remaining genes of the major coding strand of mitochondrial DNA (mtDNA). Electrophoretic mobility shift assays (EMSA) and SELEX, using mitochondrial protein extracts from cells induced to overexpress mTERF, revealed novel, weaker mTERF-binding sites, clustered in several regions of mtDNA, notably in the major non-coding region (NCR). Such binding in vivo was supported by mtDNA immunoprecipitation. Two-dimensional neutral agarose gel electrophoresis (2DNAGE) and 5' end mapping by ligation-mediated PCR (LM-PCR) identified the region of the canonical mTERF-binding site as a replication pause site. The strength of pausing was modulated by the expression level of mTERF. mTERF overexpression also affected replication pausing in other regions of the genome in which mTERF binding was found. These results indicate a role for TERF in mtDNA replication, in addition to its role in transcription. We suggest that mTERF could provide a system for coordinating the passage of replication and transcription complexes, analogous with replication pause-region binding proteins in other systems, whose main role is to safeguard the integrity of the genome whilst facilitating its efficient expression

Mammalian Mitochondrial DNA Replication Intermediates Are Essentially Duplex but Contain Extensive Tracts of RNA/DNA Hybrid

We demonstrate, using transmission electron microscopy and immunopurification with an antibody specific for RNA/DNA hybrid, that intact mtDNA replication intermediates (mtRIs) are essentially duplex throughout their length, but contain extensive RNA tracts on one strand. However, the extent of preservation of RNA in such molecules is highly dependent on the preparative method used. These findings strongly support the strand-coupled model of mtDNA replication involving RNA incorporation throughout the lagging strand (RITOLS)

A molecular-based identification resource for the arthropods of Finland

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.Peer reviewe

A molecular-based identification resource for the arthropods of Finland

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.</p

The thin red line between species:genomic differentiation of Gymnosoma Meigen, a taxonomically challenging genus of parasitoid flies (Diptera: Tachinidae)

Abstract In traditional taxonomy, species are differentiated using morphological arguments, which can be subjective and cause confusion particularly when the initial species descriptions have been inadequate. The development of DNA-based methods has provided more objective tools to recognize and quantify species differences, as well as enabled the detection of cryptic that is morphologically indistinguishable, species. Conversely, we show here that large-scale, genome-wide analysis of 11 427 loci and 65 825 SNPs is mostly unable to differentiate between many of the currently valid Palearctic species of bug-killing parasitoid flies in the genus Gymnosoma Meigen (Diptera: Tachinidae), despite the proposed morphological differences. We conclude that alongside a few well-defined taxa with discrete morphological features and unique DNA barcodes, Palearctic Gymnosoma is likely to contain a single, highly variable and geographically widespread species

Promiscuous specialists:host specificity patterns among generalist louse flies

Abstract Ectoparasites such as louse flies (Diptera: Hippoboscidae) have tendency for host specialization, which is driven by adaptation to host biology as well as competition avoidance between parasites of the same host. However, some louse fly species, especially in genera attacking birds, show wide range of suitable hosts. In the presented study, we have surveyed the current status of bird specific louse flies in Finland to provide comprehensive host association data to analyse the ecological requirements of the generalist species. A thorough sampling of 9342 birds, representing 134 species, recovered 576 specimens of louse flies, belonging to six species: Crataerina hirundinis, C. pallida, Ornithomya avicularia, O. chloropus, O. fringillina and Ornithophila metallica. Despite some overlapping hosts, the three Ornithomya species showed a notable pattern in their host preference, which was influenced not only by the host size but also by the habitat and host breeding strategy. We also provide DNA barcodes for ten Finnish species of Hippoboscidae, which can be used as a resource for species identification as well as metabarcoding studies in the future

The monophyly of the Glaurocarini (Diptera: Tachinidae: Tachininae) with the description of a new species of Semisuturia from Australia

The Glaurocarini are a small Old World tribe of tachinids belonging to the subfamily Tachininae. Two genera are currently recognized, Glaurocara Thomson with 16 species and Semisuturia Malloch with eight species. In this study we describe Semisuturia moffattensis Inclán, O'Hara, Stireman & Cerretti sp. n. from Queensland and New South Wales and compare it with congeners as well as other glaurocarines. The new species is readily identifiable among world glaurocarines by having a row of setae on lower 2/3 of facial ridge. We further evaluate the monophyly of the Glaurocarini on the basis of morphological characters of both adult and larval stages. A molecular phylogenetic analysis also supports monophyly of the tribe but does not support a close relationship between Glaurocarini and Ormiini as has been suggested previously. Finally, we provide new morphological evidence from both adults and first instar larvae to support the monophyly of both Semisuturia and Glaurocar

The Monophyly of the Glaurocarini (Diptera: Tachinidae: Tachininae) With the Description of a New Species of Semisuturia From Australia

The Glaurocarini are a small Old World tribe of tachinids belonging to the subfamily Tachininae. Two genera are currently recognized, Glaurocara Thomson with 16 species and Semisuturia Malloch with eight species. In this study we describe Semisuturia moffattensis Inclán, O’Hara, Stireman & Cerretti sp. n. from Queensland and New South Wales and compare it with congeners as well as other glaurocarines. The new species is readily identifiable among world glaurocarines by having a row of setae on lower 2/3 of facial ridge. We further evaluate the monophyly of the Glaurocarini on the basis of morphological characters of both adult and larval stages. A molecular phylogenetic analysis also supports monophyly of the tribe but does not support a close relationship between Glaurocarini and Ormiini as has been suggested previously. Finally, we provide new morphological evidence from both adults and first instar larvae to support the monophyly of both Semisuturia and Glaurocara

The Monophyly of the Glaurocarini (Diptera: Tachinidae: Tachininae) With the Description of a New Species of Semisuturia From Australia

The Glaurocarini are a small Old World tribe of tachinids belonging to the subfamily Tachininae. Two genera are currently recognized, Glaurocara Thomson with 16 species and Semisuturia Malloch with eight species. In this study we describe Semisuturia moffattensis Inclán, O’Hara, Stireman & Cerretti sp. n. from Queensland and New South Wales and compare it with congeners as well as other glaurocarines. The new species is readily identifiable among world glaurocarines by having a row of setae on lower 2/3 of facial ridge. We further evaluate the monophyly of the Glaurocarini on the basis of morphological characters of both adult and larval stages. A molecular phylogenetic analysis also supports monophyly of the tribe but does not support a close relationship between Glaurocarini and Ormiini as has been suggested previously. Finally, we provide new morphological evidence from both adults and first instar larvae to support the monophyly of both Semisuturia and Glaurocara