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Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data
The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the s...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025161/ https://www.ncbi.nlm.nih.gov/pubmed/27632164 http://dx.doi.org/10.1371/journal.pone.0163059 |
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author | Coombe, Lauren Warren, René L. Jackman, Shaun D. Yang, Chen Vandervalk, Benjamin P. Moore, Richard A. Pleasance, Stephen Coope, Robin J. Bohlmann, Joerg Holt, Robert A. Jones, Steven J. M. Birol, Inanc |
author_facet | Coombe, Lauren Warren, René L. Jackman, Shaun D. Yang, Chen Vandervalk, Benjamin P. Moore, Richard A. Pleasance, Stephen Coope, Robin J. Bohlmann, Joerg Holt, Robert A. Jones, Steven J. M. Birol, Inanc |
author_sort | Coombe, Lauren |
collection | PubMed |
description | The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis). Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly. |
format | Online Article Text |
id | pubmed-5025161 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-50251612016-09-27 Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data Coombe, Lauren Warren, René L. Jackman, Shaun D. Yang, Chen Vandervalk, Benjamin P. Moore, Richard A. Pleasance, Stephen Coope, Robin J. Bohlmann, Joerg Holt, Robert A. Jones, Steven J. M. Birol, Inanc PLoS One Research Article The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis). Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly. Public Library of Science 2016-09-15 /pmc/articles/PMC5025161/ /pubmed/27632164 http://dx.doi.org/10.1371/journal.pone.0163059 Text en © 2016 Coombe et al http://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/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Coombe, Lauren Warren, René L. Jackman, Shaun D. Yang, Chen Vandervalk, Benjamin P. Moore, Richard A. Pleasance, Stephen Coope, Robin J. Bohlmann, Joerg Holt, Robert A. Jones, Steven J. M. Birol, Inanc Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title | Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title_full | Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title_fullStr | Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title_full_unstemmed | Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title_short | Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data |
title_sort | assembly of the complete sitka spruce chloroplast genome using 10x genomics’ gemcode sequencing data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025161/ https://www.ncbi.nlm.nih.gov/pubmed/27632164 http://dx.doi.org/10.1371/journal.pone.0163059 |
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