Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)

We assembled the plastomes of Pinus greggii, P. jaliscana and P. oocarpa from 100 bp paired-end Illumina reads. We combined de novo (comparing Velvet and SPAdes) with reference-guided assembly and a final step of gap filling. SPAdes performed better than Velvet based on scaffold number (180 vs. 263)...

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Detalles Bibliográficos
Autores principales: Aguirre-Dugua, Xitlali, Gernandt, David S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2017
Materias:
Mito Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799579/
https://www.ncbi.nlm.nih.gov/pubmed/33473901
http://dx.doi.org/10.1080/23802359.2017.1365637
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author Aguirre-Dugua, Xitlali
Gernandt, David S.
author_facet Aguirre-Dugua, Xitlali
Gernandt, David S.
author_sort Aguirre-Dugua, Xitlali
collection PubMed
description We assembled the plastomes of Pinus greggii, P. jaliscana and P. oocarpa from 100 bp paired-end Illumina reads. We combined de novo (comparing Velvet and SPAdes) with reference-guided assembly and a final step of gap filling. SPAdes performed better than Velvet based on scaffold number (180 vs. 263) and mean length (1886 vs. 560 bp), and number of gaps (2 vs. 4). Annotations were automatically transferred from P. taeda NC_021440 and carefully revised by hand. Phylogenetic analysis with additional plastomes revealed very short branch lengths, supporting a rapid diversification within Australes and close relatedness among pines from Western Mexico.
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spelling pubmed-77995792021-01-19 Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes) Aguirre-Dugua, Xitlali Gernandt, David S. Mitochondrial DNA B Resour Mito Communication We assembled the plastomes of Pinus greggii, P. jaliscana and P. oocarpa from 100 bp paired-end Illumina reads. We combined de novo (comparing Velvet and SPAdes) with reference-guided assembly and a final step of gap filling. SPAdes performed better than Velvet based on scaffold number (180 vs. 263) and mean length (1886 vs. 560 bp), and number of gaps (2 vs. 4). Annotations were automatically transferred from P. taeda NC_021440 and carefully revised by hand. Phylogenetic analysis with additional plastomes revealed very short branch lengths, supporting a rapid diversification within Australes and close relatedness among pines from Western Mexico. Taylor & Francis 2017-08-22 /pmc/articles/PMC7799579/ /pubmed/33473901 http://dx.doi.org/10.1080/23802359.2017.1365637 Text en © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. 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 work is properly cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Mito Communication
Aguirre-Dugua, Xitlali
Gernandt, David S.
Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title_full Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title_fullStr Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title_full_unstemmed Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title_short Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)
title_sort complete plastomes of three endemic mexican pine species (pinus subsection australes)
topic Mito Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799579/
https://www.ncbi.nlm.nih.gov/pubmed/33473901
http://dx.doi.org/10.1080/23802359.2017.1365637
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