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

Birgit Kersten, Patricia Faivre Rampant, Malte Mader, Marie-Christine Le Paslier, Rémi Bounon, Aurélie Berard, Cristina Vettori, Hilke Schroeder, Jean-Charles Leplé, Matthias Fladung
doi: https://doi.org/10.1101/035899
Birgit Kersten
1Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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  • For correspondence: birgit.kersten@ti.bund.de
Patricia Faivre Rampant
2URGV-Plant Genomics Research, INRA, Evry, France
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Malte Mader
3Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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Marie-Christine Le Paslier
2URGV-Plant Genomics Research, INRA, Evry, France
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Rémi Bounon
2URGV-Plant Genomics Research, INRA, Evry, France
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Aurélie Berard
2URGV-Plant Genomics Research, INRA, Evry, France
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Cristina Vettori
4Institute of Bioscience and Bioresources (IBBR), National Research Council, Sesto Fiorentino, Italy
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Hilke Schroeder
1Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
3Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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Jean-Charles Leplé
5Research Unit AGPF, INRA, Orléans, France
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Matthias Fladung
1Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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Abstract

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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Posted January 04, 2016.
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Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
Birgit Kersten, Patricia Faivre Rampant, Malte Mader, Marie-Christine Le Paslier, Rémi Bounon, Aurélie Berard, Cristina Vettori, Hilke Schroeder, Jean-Charles Leplé, Matthias Fladung
bioRxiv 035899; doi: https://doi.org/10.1101/035899
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Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
Birgit Kersten, Patricia Faivre Rampant, Malte Mader, Marie-Christine Le Paslier, Rémi Bounon, Aurélie Berard, Cristina Vettori, Hilke Schroeder, Jean-Charles Leplé, Matthias Fladung
bioRxiv 035899; doi: https://doi.org/10.1101/035899

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