Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
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 appr...
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doaj-2358dae7637c49c5a5e5beea2edd683a2020-11-24T23:46:43ZengPeerJ Inc.PeerJ2167-83592017-01-015e295110.7717/peerj.2951Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomesRebecca B. Dikow0Paul B. Frandsen1Mauren Turcatel2Torsten Dikow3Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, Washington, D.C., United States of AmericaOffice of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, Washington, D.C., United States of AmericaDepartment of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of AmericaDepartment of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of AmericaA 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.https://peerj.com/articles/2951.pdfTranscriptomicsAsilidaeDraft genomeGenomicsPhylogenomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rebecca B. Dikow Paul B. Frandsen Mauren Turcatel Torsten Dikow |
spellingShingle |
Rebecca B. Dikow Paul B. Frandsen Mauren Turcatel Torsten Dikow Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes PeerJ Transcriptomics Asilidae Draft genome Genomics Phylogenomics |
author_facet |
Rebecca B. Dikow Paul B. Frandsen Mauren Turcatel Torsten Dikow |
author_sort |
Rebecca B. Dikow |
title |
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes |
title_short |
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes |
title_full |
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes |
title_fullStr |
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes |
title_full_unstemmed |
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes |
title_sort |
genomic and transcriptomic resources for assassin flies including the complete genome sequence of proctacanthus coquilletti (insecta: diptera: asilidae) and 16 representative transcriptomes |
publisher |
PeerJ Inc. |
series |
PeerJ |
issn |
2167-8359 |
publishDate |
2017-01-01 |
description |
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. |
topic |
Transcriptomics Asilidae Draft genome Genomics Phylogenomics |
url |
https://peerj.com/articles/2951.pdf |
work_keys_str_mv |
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