Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes

Rebecca B Dikow; Paul B Frandsen; Mauren Turcatel; Torsten Dikow

doi:10.7717/peerj.2951

Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes

PeerJ. 2017 Jan 31:5:e2951. doi: 10.7717/peerj.2951. eCollection 2017.

Authors

Rebecca B Dikow¹, Paul B Frandsen¹, Mauren Turcatel², Torsten Dikow²

Affiliations

¹ Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution , Washington , D.C. , United States of America.
² Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washington , D.C. , United States of America.

Abstract

A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.

Keywords: Asilidae; Draft genome; Genomics; Phylogenomics; Transcriptomics.

Grants and funding

This work was supported by start-up funds provided by the Smithsonian Institution National Museum of Natural History to TD, by the Smithsonian Institution Global Genome Initiative (GGI) for a project entitled “Asiloid flies in the Nama Karoo and comparative phylogenomics” (No. 33GGI2014GRANTA-DikowT) to TD and a project entitled “Genomic Collection of Horse Flies (Diptera: Tabanidae) of the Amazon Rainforest” (No. 33GGI2015GRANTR-TurcatelM) to MT, the NMNH Diptera Sabrosky Endowment (with contributions by H Williams) to TD, and access to in-kind sequencing by the NMNH Laboratories of Analytical Biology (LAB). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.