title: Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.
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.
authors.affiliation: Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Kersten
authors.affiliation: URGV-Plant Genomics Research, INRA, Evry, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Faivre Rampant
authors.affiliation: Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
authors.forename: Malte
authors.initials: M
authors.lastname: Mader
authors.affiliation: URGV-Plant Genomics Research, INRA, Evry, France.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.affiliation: URGV-Plant Genomics Research, INRA, Evry, France.
authors.forename: Rémi
authors.initials: R
authors.lastname: Bounon
authors.affiliation: URGV-Plant Genomics Research, INRA, Evry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Berard
authors.affiliation: Institute of Bioscience and Bioresources (IBBR), National Research Council, Sesto Fiorentino, Italy.
authors.forename: Cristina
authors.initials: C
authors.lastname: Vettori
authors.affiliation: Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.|Ecological Genetics, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
authors.forename: Hilke
authors.initials: H
authors.lastname: Schroeder
authors.affiliation: Research Unit AGPF, INRA, Orléans, France.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Leplé
authors.affiliation: Genome Research, Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Fladung
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D018745:Genome, Plant; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D000069600:Plant Breeding; D032107:Populus / Q000145:classification / Q000235:genetics*