Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.
ABSTRACT: The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.
Project description:Blue shining fungus gnats (Diptera) had been long reported in the Waitomo caves of New Zealand (Arachnocampa luminosa Skuse), in stream banks of the American Appalachian Mountains (Orfelia fultoni Fisher) in 1939 and in true spore eating Eurasiatic Keroplatus Bosc species. This current report observes that similar blue light emitting gnat larvae also occur nearby the Betary river in the buffer zone of High Ribeira River State Park (PETAR) in the Atlantic Forest of Brazil, where the larvae were found when on fallen branches or trunks enveloped in their own secreted silk. The new species is named Neoceroplatus betaryiensis nov. sp. (Diptera: Keroplatidae: Keroplatinae: Keroplatini) based on a morphological analysis. Neoceroplatus betaryiensis nov. sp. larvae emit blue bioluminescence that can be seen from their last abdominal segment and from two photophores located laterally on the first thoracic segment. When touched, the larvae can actively stop its luminescence, which returns when it is no longer being agitated. The in vitro bioluminescence spectrum of N. betaryiensis nov. sp. peaks at 472?nm, and cross-reactivity of hot and cold extracts with the luciferin-luciferase from Orfelia fultoni indicate significant similarity in both enzyme and substrate of the two species, and that the bioluminescence system in the subfamily Keroplatinae is conserved.
Project description:The following 17 extant new species of Sciaroidea (Diptera: Bibionomorpha) are described: <i>Bolitophila nikolae</i> Ševčík sp. nov. (Bolitophilidae, Taiwan), <i>Catocha jingfui</i> sp. nov. (Cecidomyiidae, Taiwan), <i>Catocha manmiaoe</i> sp. nov. (Cecidomyiidae, Taiwan), <i>Catocha shengfengi</i> sp. nov. (Cecidomyiidae, Taiwan), <i>Planetella taiwanensis</i> sp. nov. (Cecidomyiidae, Taiwan), <i>Diadocidia pseudospinusola</i> sp. nov. (Diadocidiidae, Taiwan), <i>Asioditomyia bruneicola</i> sp. nov. (Ditomyiidae, Brunei), <i>Asioditomyia lacii</i> sp. nov. (Ditomyiidae, Taiwan), <i>Ditomyia asiatica</i> sp. nov. (Ditomyiidae, Thailand), <i>Chetoneura davidi</i> sp. nov. (Keroplatidae, Brunei), <i>Euceroplatus mantici</i> sp. nov. (Keroplatidae, Thailand), <i>Setostylus fangshuoi</i> sp. nov. (Keroplatidae, Taiwan), <i>Platyceridion yunfui</i> sp. nov. (Keroplatidae, Hainan), <i>Terocelion adami</i> sp. nov. (Keroplatidae, Taiwan), <i>Hadroneura martini</i> sp. nov. (Mycetophilidae, Taiwan), <i>Paratinia furcata</i> sp. nov. (Mycetophilidae, Czech Republic, Slovakia), and <i>Nepaletricha sikorai</i> sp. nov. (Sciaroidea incertae sedis, Thailand). Two new genera are described from the mid-Cretaceous Burmese amber, <i>Burmasymmerus</i> gen. nov. (Ditomyiidae, type species <i>Burmasymmerus korneliae</i> sp. nov., including also <i>B. wieslawi</i> sp. nov.), representing the first record of the family Ditomyiidae from the Mesozoic, and <i>Burmatricha</i> gen. nov. (Sciaroidea incertae sedis, type species <i>Burmatricha mesozoica</i> sp. nov.). Molecular phylogeny of Ditomyiidae, based on two DNA markers (28S, COI), as well as that of <i>Catocha</i> Haliday, 1833, based on the mitochondrial COI and 16S fragments, are also presented.
Project description:<h4>Background</h4><i>Holorusia</i> Loew, 1863 (Diptera: Tipulidae) is a relatively large crane fly genus with a wide distribution in the Afrotropic, Australasian-Oceanian, Eastern Palearctic, Oriental and Nearctic Regions. Although the genus is well known to include the largest crane fly species, the immature stages are, thus far, only described for the larva and pupa of the North American <i>Holorusia hesperea</i> Arnaud & Byers, 1990.<h4>New information</h4>In this study, we describe for the first time the egg, larva and pupae of the Japanese <i>Holorusia mikado</i> (Westwood, 1876). Larvae were collected from semi-aquatic habitats, from slow flowing areas of streams and small waterfalls where leaf litter accumulates; the larvae are detritivores and feed on wet, decomposing leaves. The larvae were reared to adults in the laboratory. Morphological characters of immature stages discussed with comparison with the North American <i>H. hespera</i>. Male and female genitalia are illustrated and described in detail for the first time.
Project description:<i>Chrysomya nigripes</i> (Diptera: Calliphoridae) is a blow fly species of forensic importance. Here we demonstrated the complete mitochondrial genome of this species for the first time. Phylogenetic analyses indicated that entire mitochondrial genome sequences can provide more useful information for distinguishing <i>C. nigripes</i> from the other species.
Project description:A new species of crane fly (Diptera, Limoniidae), Elephantomyia (Elephantomyia) hallasana Podenas & Podeniene, sp. nov., from Jeju Island, South Korea is described. Adult and larval characters are illustrated. Elephantomyia (E.) hallasanasp. nov. is the only species of the genus Elephantomyia Osten Sacken, 1860 recorded from Jeju Island, South Korea. Habitat, elevation range, and seasonality data are presented. Distributional notes on E. subterminalis Alexander, 1954 in the Far East of Russia (Khabarovskiy and Primorskiy regions) are discussed. An identification key for all Eastern Palaearctic species of subgenus E. (Elephantomyia) is presented.
Project description:Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
Project description:This is the first study to report Chrysomya pinguis (Walker) and Lucilia porphyrina (Walker) (Diptera: Calliphoridae) as forensically important blow fly species from human cadavers in Thailand, in addition to Chrysomya villeneuvi (Patton) already known in Thailand. In 2016, a fully decomposed body of an unknown adult male was discovered in a high mountainous forest during winter in Chiang Mai province. The remains were infested heavily with thousands of blow fly larvae feeding simultaneously on them. Morphological identification of adults reared from the larvae, and molecular analysis based on sequencing of 1,247 bp partial mitochondrial cytochrome c oxidase subunit 1 gene (CO1) of the larvae and puparia, confirmed the above mentioned 3 species. The approving forensic fly evidence by molecular approach was described for the first time in Thailand. Moreover, neighbor-joining phylogenetic analysis of the CO1 was performed to compare the relatedness of the species, thereby affirming the accuracy of identification. As species of entomofauna varies among cases in different geographic and climatic circumstances, C. pinguis and L. porphyrina were added to the list of Thai forensic entomology caseworks, including colonizers of human remains in open, high mountainous areas during winter. Further research should focus on these 3 species, for which no developmental data are currently available.
Project description:Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.
Project description:The phylogeny of the insect infraorder Bibionomorpha (Diptera) is reconstructed based on the combined analysis of three nuclear (18S, 28S, CAD) and three mitochondrial (12S, 16S, COI) gene markers. All the analyses strongly support the monophyly of Bibionomorpha in both the narrow (<i>sensu stricto</i>) and the broader (<i>sensu lato</i>) concepts. The major lineages of Bibionomorpha <i>sensu lato</i> (Sciaroidea, Bibionoidea, Anisopodoidea, and Scatopsoidea) and most of the included families are supported as monophyletic groups. Axymyiidae was not found to be part of Bibionomorpha nor was it found to be its sister group. Bibionidae was paraphyletic with respect to Hesperinidae and Keroplatidae was paraphyletic with respect to Lygistorrhinidae. The included Sciaroidea <i>incertae sedis</i> (except <i>Ohakunea</i> Edwards) were found to belong to one clade, but the relationships within this group and its position within Sciaroidea require further study.
Project description:Larvae of O. fultoni (Keroplatidae: Keroplatinae), which occur along river banks in the Appalachian Mountains in Eastern United States, produce the bluest bioluminescence among insects from translucent areas associated to black bodies, which are located mainly in the anterior and posterior parts of the body. Although closely related to Arachnocampa spp (Keroplatidae: Arachnocampininae), O.fultoni has a morphologically and biochemically distinct bioluminescent system which evolved independently, requiring a luciferase enzyme, a luciferin, a substrate binding fraction (SBF) that releases luciferin in the presence of mild reducing agents, molecular oxygen, and no additional cofactors. Similarly, the closely related Neoceroplatus spp, shares the same kind of luciferin-luciferase system of Orfelia fultoni. However, the molecular properties, identities and functions of luciferases, SBF and luciferin of Orfelia fultoni and other luminescent members of the Keroplatinae subfamily still remain to be fully elucidated. Using O. fultoni as a source of luciferase, and the recently discovered non-luminescent cave worm Neoditomiya sp as the main source of luciferin and SBF, we isolated and initially characterized these compounds. The luciferase of O. fultoni is a stable enzyme active as an apparent trimer (220 kDa) composed of ~70 kDa monomers, with an optimum pH of 7.8. The SBF, which is found in the black bodies in Orfelia fultoni and in smaller dark granules in Neoditomiya sp, consists of a high molecular weight complex of luciferin and proteins, apparently associated to mitochondria. The luciferin, partially purified from hot extracts by a combination of anion exchange chromatography and TLC, is a very polar and weakly fluorescent compound, whereas its oxidized product displays blue fluorescence with an emission spectrum matching the bioluminescence spectrum (~460 nm), indicating that it is oxyluciferin. The widespread occurrence of luciferin and SBF in both luminescent and non-luminescent Keroplatinae larvae indicate an additional important biological function for the substrate, and therefore the name keroplatin.