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Improved contiguity of the threespine stickleback genome using long-read sequencing
While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contig...
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/PMC8022941/ https://www.ncbi.nlm.nih.gov/pubmed/33598708 http://dx.doi.org/10.1093/g3journal/jkab007 |
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author | Nath, Shivangi Shaw, Daniel E White, Michael A |
author_facet | Nath, Shivangi Shaw, Daniel E White, Michael A |
author_sort | Nath, Shivangi |
collection | PubMed |
description | While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish. |
format | Online Article Text |
id | pubmed-8022941 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-80229412021-04-09 Improved contiguity of the threespine stickleback genome using long-read sequencing Nath, Shivangi Shaw, Daniel E White, Michael A G3 (Bethesda) Genome Report While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish. Oxford University Press 2021-01-23 /pmc/articles/PMC8022941/ /pubmed/33598708 http://dx.doi.org/10.1093/g3journal/jkab007 Text en © The Author(s) 2021. 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 (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 | Genome Report Nath, Shivangi Shaw, Daniel E White, Michael A Improved contiguity of the threespine stickleback genome using long-read sequencing |
title | Improved contiguity of the threespine stickleback genome using long-read sequencing |
title_full | Improved contiguity of the threespine stickleback genome using long-read sequencing |
title_fullStr | Improved contiguity of the threespine stickleback genome using long-read sequencing |
title_full_unstemmed | Improved contiguity of the threespine stickleback genome using long-read sequencing |
title_short | Improved contiguity of the threespine stickleback genome using long-read sequencing |
title_sort | improved contiguity of the threespine stickleback genome using long-read sequencing |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022941/ https://www.ncbi.nlm.nih.gov/pubmed/33598708 http://dx.doi.org/10.1093/g3journal/jkab007 |
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