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Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq
Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Se...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258696/ https://www.ncbi.nlm.nih.gov/pubmed/30479362 http://dx.doi.org/10.1038/s41598-018-35654-3 |
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author | Osuna-Mascaró, Carolina Rubio de Casas, Rafael Perfectti, Francisco |
author_facet | Osuna-Mascaró, Carolina Rubio de Casas, Rafael Perfectti, Francisco |
author_sort | Osuna-Mascaró, Carolina |
collection | PubMed |
description | Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Seq instead of genomic DNA libraries remains to be thoroughly verified. In this study, we assembled chloroplast genomes for three Erysimum (Brassicaceae) species from three RNA-Seq replicas and from one genomic library of each species, using a streamlined bioinformatics protocol. We compared these assembled genomes, confirming that assembled cp genomes from RNA-Seq data were highly similar to each other and to those from genomic libraries in terms of overall structure, size, and composition. Although post-transcriptional modifications, such as RNA-editing, may introduce variations in the RNA-seq data, the assembly of cp genomes from RNA-seq appeared to be reliable. Moreover, RNA-Seq assembly was less sensitive to sources of error such as the recovery of nuclear plastid DNAs (NUPTs). Although some precautions should be taken when producing reference genomes in non-model plants, we conclude that assembling cp genomes from RNA-Seq data is a fast, accurate, and reliable strategy. |
format | Online Article Text |
id | pubmed-6258696 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62586962018-12-03 Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq Osuna-Mascaró, Carolina Rubio de Casas, Rafael Perfectti, Francisco Sci Rep Article Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Seq instead of genomic DNA libraries remains to be thoroughly verified. In this study, we assembled chloroplast genomes for three Erysimum (Brassicaceae) species from three RNA-Seq replicas and from one genomic library of each species, using a streamlined bioinformatics protocol. We compared these assembled genomes, confirming that assembled cp genomes from RNA-Seq data were highly similar to each other and to those from genomic libraries in terms of overall structure, size, and composition. Although post-transcriptional modifications, such as RNA-editing, may introduce variations in the RNA-seq data, the assembly of cp genomes from RNA-seq appeared to be reliable. Moreover, RNA-Seq assembly was less sensitive to sources of error such as the recovery of nuclear plastid DNAs (NUPTs). Although some precautions should be taken when producing reference genomes in non-model plants, we conclude that assembling cp genomes from RNA-Seq data is a fast, accurate, and reliable strategy. Nature Publishing Group UK 2018-11-27 /pmc/articles/PMC6258696/ /pubmed/30479362 http://dx.doi.org/10.1038/s41598-018-35654-3 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Osuna-Mascaró, Carolina Rubio de Casas, Rafael Perfectti, Francisco Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title | Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title_full | Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title_fullStr | Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title_full_unstemmed | Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title_short | Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq |
title_sort | comparative assessment shows the reliability of chloroplast genome assembly using rna-seq |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258696/ https://www.ncbi.nlm.nih.gov/pubmed/30479362 http://dx.doi.org/10.1038/s41598-018-35654-3 |
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