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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Bibliographic Details
Published in:PloS one 2016-01, Vol.11 (1), p.e0147209-e0147209
Main Authors: Kersten, Birgit, Faivre Rampant, Patricia, Mader, Malte, Le Paslier, Marie-Christine, Bounon, Rémi, Berard, Aurélie, Vettori, Cristina, Schroeder, Hilke, Leplé, Jean-Charles, Fladung, Matthias
Format: Article
Language:English
Subjects:
Apoptosis
Biology and Life Sciences
Breeding
Chloroplast DNA
Chloroplasts
Chloroplasts - genetics
Cloning
Deoxyribonucleic acid
DNA
DNA sequencing
Evolution
Flowers & plants
Gene sequencing
Genes
Genetic engineering
Genetic testing
Genome, Plant
Genomes
Genomics
Life Sciences
Mitochondria
Mitochondria - genetics
Mitochondrial DNA
Nuclei
Nucleotide sequence
Organelles
Phylogeny
Plant Breeding
Poplar
Populus - classification
Populus - genetics
Research and Analysis Methods
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Vegetal Biology
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0147209