Dataset Information

The genome sequence of a hoverfly, Sphaerophoria taeniata (Meigen, 1822).

ABSTRACT: We present a genome assembly from an individual male Sphaerophoria taeniata (a hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 609.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.42 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,213 protein coding genes.

SUBMITTER: Falk S

PROVIDER: S-EPMC10905010 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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The genome sequence of a hoverfly, <i>Sphaerophoria taeniata</i> (Meigen, 1822).

Falk Steven S Sudworth Jennifer J

Wellcome open research 20231018

We present a genome assembly from an individual male <i>Sphaerophoria taeniata</i> (a hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 609.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.42 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,213 protein coding genes. ...[more]

PMID: 38434738

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Project description:Micro-computed tomography (micro-CT) is an X-ray-based technique that allows visualisation of the internal anatomy of insects in situ and does not require dissections. Traditionally, the study of insect anatomy has been mainly based on dissection techniques and microtome sections. However, micro-CT is becoming an increasingly widespread study technique. We report the use of micro-CT scans to study, in detail, the external and internal structures and organs of the third instar larva of the dipteran Syrphidae Sphaerophoria rueppellii, a Palaearctic species included in the list of effective agents used in European biocontrol programmes against aphids. Detailed images and videos provided evidence of the external morphological characteristics and an overview of the internal anatomy (musculature, digestive tube, salivary glands, Malpighian tubules, fat body, circulatory system, nervous system, cephalopharyngeal complex, tentorium, and mouth parts). The study evidenced the following: an external lateroventral complex of muscles that form muscular rings that allow the compression of the body segments in a similar functional way as occurs in annelid worms; the existence of mandibles with prosthecae; the nervous system present a conspicuous distinguishable suboesophageal ganglion; the so-called antennomaxillary organs are the antennae; the maxillae are separate structures, with an articulated maxillary palpus; S. rueppellii has only one pair of Malpighian tubules instead of the two pairs that were thought to be the general rule for Syrphid larvae; and the evidence of an imaginal disc of genitalia in the posterior part of the body, below the rectum, which in male larvae has a clear correspondence with the morphology of the external male genitalia, which allows to differentiate the sexes in the larval stage. This study constitutes a true anatomical atlas of the third instar larvae of S. rueppellii. High-quality rendered images and additional supplementary videos together with a 3D model, suitable for use with mobile devices, are useful tools for future research and teaching aids.

Project description:BackgroundSphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs).Methods and findingsIn this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species.Conclusion and significanceThis assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.

Dataset Information

The genome sequence of a hoverfly, Sphaerophoria taeniata (Meigen, 1822).

Publications

The genome sequence of a hoverfly, <i>Sphaerophoria taeniata</i> (Meigen, 1822).

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