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Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

SIMPLE SUMMARY: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for t...

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Autores principales: Saha, Surya, Cooksey, Amanda M., Childers, Anna K., Poelchau, Monica F., McCarthy, Fiona M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8397112/
https://www.ncbi.nlm.nih.gov/pubmed/34442314
http://dx.doi.org/10.3390/insects12080748
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author Saha, Surya
Cooksey, Amanda M.
Childers, Anna K.
Poelchau, Monica F.
McCarthy, Fiona M.
author_facet Saha, Surya
Cooksey, Amanda M.
Childers, Anna K.
Poelchau, Monica F.
McCarthy, Fiona M.
author_sort Saha, Surya
collection PubMed
description SIMPLE SUMMARY: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for the improvement of human health, agriculture, and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover, this functional annotation process must be easily accessible and provide information at a genomic scale to keep up with new sequence data. We report a well-defined workflow for rapid functional annotation of whole proteomes to produce Gene Ontology and pathways information. We test this workflow on a diverse set of arthropod genomes and compare it to common arthropod reference genomes. The workflow we described is freely and publicly available via a web interface on CyVerse or as biocontainers that can be deployed scalably on local computing systems. ABSTRACT: Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply ‘omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality.
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spelling pubmed-83971122021-08-28 Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes Saha, Surya Cooksey, Amanda M. Childers, Anna K. Poelchau, Monica F. McCarthy, Fiona M. Insects Article SIMPLE SUMMARY: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for the improvement of human health, agriculture, and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover, this functional annotation process must be easily accessible and provide information at a genomic scale to keep up with new sequence data. We report a well-defined workflow for rapid functional annotation of whole proteomes to produce Gene Ontology and pathways information. We test this workflow on a diverse set of arthropod genomes and compare it to common arthropod reference genomes. The workflow we described is freely and publicly available via a web interface on CyVerse or as biocontainers that can be deployed scalably on local computing systems. ABSTRACT: Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply ‘omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality. MDPI 2021-08-19 /pmc/articles/PMC8397112/ /pubmed/34442314 http://dx.doi.org/10.3390/insects12080748 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Saha, Surya
Cooksey, Amanda M.
Childers, Anna K.
Poelchau, Monica F.
McCarthy, Fiona M.
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title_full Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title_fullStr Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title_full_unstemmed Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title_short Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
title_sort workflows for rapid functional annotation of diverse arthropod genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8397112/
https://www.ncbi.nlm.nih.gov/pubmed/34442314
http://dx.doi.org/10.3390/insects12080748
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