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Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing
The first insect genome assembly (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a “state-of-the-fi...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358217/ https://www.ncbi.nlm.nih.gov/pubmed/34152413 http://dx.doi.org/10.1093/gbe/evab138 |
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author | Hotaling, Scott Sproul, John S Heckenhauer, Jacqueline Powell, Ashlyn Larracuente, Amanda M Pauls, Steffen U Kelley, Joanna L Frandsen, Paul B |
author_facet | Hotaling, Scott Sproul, John S Heckenhauer, Jacqueline Powell, Ashlyn Larracuente, Amanda M Pauls, Steffen U Kelley, Joanna L Frandsen, Paul B |
author_sort | Hotaling, Scott |
collection | PubMed |
description | The first insect genome assembly (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a “state-of-the-field” perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased toward four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 Mb in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long reads are ∼48× more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: 1) seek better integration between independent research groups and consortia, 2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, 3) take advantage of long-read sequencing technologies, and 4) expand and improve gene annotations. |
format | Online Article Text |
id | pubmed-8358217 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-83582172021-08-12 Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing Hotaling, Scott Sproul, John S Heckenhauer, Jacqueline Powell, Ashlyn Larracuente, Amanda M Pauls, Steffen U Kelley, Joanna L Frandsen, Paul B Genome Biol Evol Letter The first insect genome assembly (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a “state-of-the-field” perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased toward four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 Mb in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long reads are ∼48× more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: 1) seek better integration between independent research groups and consortia, 2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, 3) take advantage of long-read sequencing technologies, and 4) expand and improve gene annotations. Oxford University Press 2021-06-21 /pmc/articles/PMC8358217/ /pubmed/34152413 http://dx.doi.org/10.1093/gbe/evab138 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (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 | Letter Hotaling, Scott Sproul, John S Heckenhauer, Jacqueline Powell, Ashlyn Larracuente, Amanda M Pauls, Steffen U Kelley, Joanna L Frandsen, Paul B Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title | Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title_full | Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title_fullStr | Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title_full_unstemmed | Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title_short | Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing |
title_sort | long reads are revolutionizing 20 years of insect genome sequencing |
topic | Letter |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358217/ https://www.ncbi.nlm.nih.gov/pubmed/34152413 http://dx.doi.org/10.1093/gbe/evab138 |
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