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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...

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Detalles Bibliográficos
Autores principales: Nath, Shivangi, Shaw, Daniel E, White, Michael A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
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.
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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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