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Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x...

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Autores principales: Kersten, Birgit, Faivre Rampant, Patricia, Mader, Malte, Le Paslier, Marie-Christine, Bounon, Rémi, Berard, Aurélie, Vettori, Cristina, Schroeder, Hilke, Leplé, Jean-Charles, Fladung, Matthias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723046/
https://www.ncbi.nlm.nih.gov/pubmed/26800039
http://dx.doi.org/10.1371/journal.pone.0147209
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author Kersten, Birgit
Faivre Rampant, Patricia
Mader, Malte
Le Paslier, Marie-Christine
Bounon, Rémi
Berard, Aurélie
Vettori, Cristina
Schroeder, Hilke
Leplé, Jean-Charles
Fladung, Matthias
author_facet Kersten, Birgit
Faivre Rampant, Patricia
Mader, Malte
Le Paslier, Marie-Christine
Bounon, Rémi
Berard, Aurélie
Vettori, Cristina
Schroeder, Hilke
Leplé, Jean-Charles
Fladung, Matthias
author_sort Kersten, Birgit
collection PubMed
description Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.
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spelling pubmed-47230462016-01-30 Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding Kersten, Birgit Faivre Rampant, Patricia Mader, Malte Le Paslier, Marie-Christine Bounon, Rémi Berard, Aurélie Vettori, Cristina Schroeder, Hilke Leplé, Jean-Charles Fladung, Matthias PLoS One Research Article Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future. Public Library of Science 2016-01-22 /pmc/articles/PMC4723046/ /pubmed/26800039 http://dx.doi.org/10.1371/journal.pone.0147209 Text en © 2016 Kersten 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
Kersten, Birgit
Faivre Rampant, Patricia
Mader, Malte
Le Paslier, Marie-Christine
Bounon, Rémi
Berard, Aurélie
Vettori, Cristina
Schroeder, Hilke
Leplé, Jean-Charles
Fladung, Matthias
Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title_full Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title_fullStr Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title_full_unstemmed Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title_short Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
title_sort genome sequences of populus tremula chloroplast and mitochondrion: implications for holistic poplar breeding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723046/
https://www.ncbi.nlm.nih.gov/pubmed/26800039
http://dx.doi.org/10.1371/journal.pone.0147209
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