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Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)

Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making beh...

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Autores principales: Heckenhauer, Jacqueline, Frandsen, Paul B, Gupta, Deepak K, Paule, Juraj, Prost, Stefan, Schell, Tilman, Schneider, Julio V, Stewart, Russell J, Pauls, Steffen U
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916706/
https://www.ncbi.nlm.nih.gov/pubmed/31774498
http://dx.doi.org/10.1093/gbe/evz264
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author Heckenhauer, Jacqueline
Frandsen, Paul B
Gupta, Deepak K
Paule, Juraj
Prost, Stefan
Schell, Tilman
Schneider, Julio V
Stewart, Russell J
Pauls, Steffen U
author_facet Heckenhauer, Jacqueline
Frandsen, Paul B
Gupta, Deepak K
Paule, Juraj
Prost, Stefan
Schell, Tilman
Schneider, Julio V
Stewart, Russell J
Pauls, Steffen U
author_sort Heckenhauer, Jacqueline
collection PubMed
description Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making behavior that allows them to exploit a wide range of ecological niches. Only five genomes of this order have been published thus far, with variable qualities regarding contiguity and completeness. A low-cost sequencing strategy, that is, using a single Oxford Nanopore flow cell per individual along with Illumina sequence reads was successfully used to generate high-quality genomes of two Trichoptera species, Plectrocnemia conspersa and Hydropsyche tenuis. Of the de novo assembly methods compared, assembly of low coverage Nanopore reads (∼18×) and subsequent polishing with long reads followed by Illumina short reads (∼80–170× coverage) yielded the highest genome quality both in terms of contiguity and BUSCO completeness. The presented genomes are the shortest to date and extend our knowledge of genome size across caddisfly families. The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters. The new genomic resources presented in this paper are among the highest quality Trichoptera genomes and will increase the knowledge of this important insect order by serving as the basis for phylogenomic and comparative genomic studies.
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spelling pubmed-69167062019-12-19 Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera) Heckenhauer, Jacqueline Frandsen, Paul B Gupta, Deepak K Paule, Juraj Prost, Stefan Schell, Tilman Schneider, Julio V Stewart, Russell J Pauls, Steffen U Genome Biol Evol Genome Report Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making behavior that allows them to exploit a wide range of ecological niches. Only five genomes of this order have been published thus far, with variable qualities regarding contiguity and completeness. A low-cost sequencing strategy, that is, using a single Oxford Nanopore flow cell per individual along with Illumina sequence reads was successfully used to generate high-quality genomes of two Trichoptera species, Plectrocnemia conspersa and Hydropsyche tenuis. Of the de novo assembly methods compared, assembly of low coverage Nanopore reads (∼18×) and subsequent polishing with long reads followed by Illumina short reads (∼80–170× coverage) yielded the highest genome quality both in terms of contiguity and BUSCO completeness. The presented genomes are the shortest to date and extend our knowledge of genome size across caddisfly families. The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters. The new genomic resources presented in this paper are among the highest quality Trichoptera genomes and will increase the knowledge of this important insect order by serving as the basis for phylogenomic and comparative genomic studies. Oxford University Press 2019-11-27 /pmc/articles/PMC6916706/ /pubmed/31774498 http://dx.doi.org/10.1093/gbe/evz264 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Genome Report
Heckenhauer, Jacqueline
Frandsen, Paul B
Gupta, Deepak K
Paule, Juraj
Prost, Stefan
Schell, Tilman
Schneider, Julio V
Stewart, Russell J
Pauls, Steffen U
Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title_full Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title_fullStr Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title_full_unstemmed Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title_short Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
title_sort annotated draft genomes of two caddisfly species plectrocnemia conspersa curtis and hydropsyche tenuis navas (insecta: trichoptera)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916706/
https://www.ncbi.nlm.nih.gov/pubmed/31774498
http://dx.doi.org/10.1093/gbe/evz264
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