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Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality, and host–parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here, we present a high-quality hybrid geno...

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Autores principales: Bhattarai, Upendra R, Katuwal, Mandira, Poulin, Robert, Gemmell, Neil J, Dowle, Eddy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526046/
https://www.ncbi.nlm.nih.gov/pubmed/35972389
http://dx.doi.org/10.1093/g3journal/jkac199
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author Bhattarai, Upendra R
Katuwal, Mandira
Poulin, Robert
Gemmell, Neil J
Dowle, Eddy
author_facet Bhattarai, Upendra R
Katuwal, Mandira
Poulin, Robert
Gemmell, Neil J
Dowle, Eddy
author_sort Bhattarai, Upendra R
collection PubMed
description The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality, and host–parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here, we present a high-quality hybrid genome assembly for Forficula auricularia using Nanopore long-reads and 10× linked-reads. The final assembly is 1.06 Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55 Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ∼90% from 3 sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. Phylogenetic analysis revealed the assembled genome as that of species B, one of the 2 known genetic subspecies of Forficula auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on dermapterans.
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spelling pubmed-95260462022-10-03 Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B) Bhattarai, Upendra R Katuwal, Mandira Poulin, Robert Gemmell, Neil J Dowle, Eddy G3 (Bethesda) Genome Report The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality, and host–parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here, we present a high-quality hybrid genome assembly for Forficula auricularia using Nanopore long-reads and 10× linked-reads. The final assembly is 1.06 Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55 Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ∼90% from 3 sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. Phylogenetic analysis revealed the assembled genome as that of species B, one of the 2 known genetic subspecies of Forficula auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on dermapterans. Oxford University Press 2022-08-16 /pmc/articles/PMC9526046/ /pubmed/35972389 http://dx.doi.org/10.1093/g3journal/jkac199 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Bhattarai, Upendra R
Katuwal, Mandira
Poulin, Robert
Gemmell, Neil J
Dowle, Eddy
Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title_full Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title_fullStr Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title_full_unstemmed Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title_short Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B)
title_sort genome assembly and annotation of the european earwig forficula auricularia (subspecies b)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526046/
https://www.ncbi.nlm.nih.gov/pubmed/35972389
http://dx.doi.org/10.1093/g3journal/jkac199
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