Dataset Information

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera).

ABSTRACT: Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius' genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.

SUBMITTER: Schmidt H

PROVIDER: S-EPMC7144091 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Publications

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera).

Schmidt Hanno H Hellmann Sören Lukas SL Waldvogel Ann-Marie AM Feldmeyer Barbara B Hankeln Thomas T Pfenninger Markus M

G3 (Bethesda, Md.) 20200409 4

Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius' genome one of the most contiguous Dipteran genomes published, the first compl ...[more]

PMID: 32060047

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Project description:This study focuses on interactions between nanoparticles and a pesticide. The aim was to investigate how nano-sized aluminum oxide (410 nm) can alter the toxic effects of thiacloprid, even if no sorption between particles and the insecticide takes place. Thus, our study investigated a rather unexplored interaction. We conducted our research with larvae of Chironomus riparius and used thiacloprid as test substance as its toxicity to C. riparius is well described. The used nano-Al2O3 particles where chosen due to their suitable properties. For testing the acute effects of the interaction, we exposed larvae to thiacloprid (0.5, 1.0, 2.0, and 5.0 μg/L) and nano-Al2O3 (300 and 1000 mg/L), either solely or in binary mixtures. While thiacloprid resulted in elevated mortality, nano-Al2O3 solely did not exert any effects. Moreover, we observed an aggregation of nano-Al2O3 within the lumen of the intestinal tract of the larvae. Further results showed a significantly reduced mortality of fourth instar larvae when they were exposed to mixtures of nanoparticles and the pesticide, compared to thiacloprid alone. With increasing nano-Al2O3 concentration, this effect became gradually stronger. Additionally, chemical analyses of internal thiacloprid concentrations implicate reduced uptake of thiacloprid in animals exposed to mixtures. However, as larvae exposed to thiacloprid concentrations > 0.5 μg/L showed severe convulsions, independent of the presence or concentration of nano-Al2O3, we assume that nano-Al2O3 leads to a delay of mortality and does not entirely prevent it. As sorption measurements on pristine or defecated nano-Al2O3 did not reveal any sorptive interaction with thiacloprid, we can exclude sorption-based reduction of thiacloprid bioavailability as a mechanism behind our results. Even though we used test substances which might not co-occur in the environment in the tested concentrations, our study gives evidence for an interaction besides adsorption, which is important to generally understand how nanoparticles might affect biota.

Project description:Background Representatives of the family Chironomidae (non-biting midges; order Diptera) are found worldwide. Freeze-dried chironomid larvae, predominantly of the species Chironomus thummi thummi are frequently used as fish food and are an allergen source for fish keepers and persons employed in the manufacture of fish food. At present, 9 allergens of C. thummi thummi have been assigned an official designation by the WHO/IUIS allergen nomenclature sub-committee: Chi t 1 to 9. All of them are hemoglobins with molecular weights of 16 kDa. IgE binding and cross-reactivity was clearly demonstrated for all these proteins. However, the assignment of 9 distinct allergen numbers to members of the same protein family is quite unusual. Methods Currently, the IUIS allergen database contains 12 allergen and isoallergen sequences from C. thummi thummi. The Uniprot database has demerged entry P02225, listed in the database for Chi t 7, into 7 entries, 5 from C. thummi thummi and 2 from C. thummi piger that are identical to 2 of the sequences from C. thummi thummi. Consequently, the 16 unique amino acid sequences of the mature C. thummi allergens were aligned using ClustalX2, a neighbor-joining tree was generated from the alignment and a percent sequence identity matrix was built to evaluate appropriate nomenclature. Results Pairwise sequence alignments showed that sequences belonging to allergens Chi t 5, 6, 7 and 8 possess sequence identities to Chi t 3 of between 51 and 63%. Chi t 1, 2, 4, and 9 diverge to a greater extent from Chi t 3 (<50% identical) and from each other. Phylogenetic tree analysis suggests the clustering of Chi t 3, 6, 7, and 8, while Chi t 1, 2, 4, 5, and 9 form separate clades. Conclusions Based on these analyses, the IUIS Allergen Nomenclature Sub-Committee renames Chi t 5, 6, 7 and 8 isoallergens of Chi t 3, even though their sequence identities to Chi t 3 are below the 67% threshold previously defined for isoallergens. The remaining hemoglobins, previously designated Chi t 1, 2, 4 and 9 will retain their previous names.

Dataset Information

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera).

Publications

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge <i>Chironomus riparius</i> (Diptera).

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