<abstract xmlns="http://www.w3.org/1999/xhtml"><p><italic>Populus trichocarpa</italic> and <italic>P. deltoides</italic> are the only <italic>Populus</italic> species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (<ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://phytozome.jgi.doe.gov/">https://phytozome.jgi.doe.gov/</ext-link>). Here we focus on the clone INRA 717-1B4, a female <italic>P. tremula x P. alba</italic> (<italic>P. x canescens</italic>) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1.1 of sPta717 at <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://aspendb.uga.edu/index.php/databases/spta-717-genome">http://aspendb.uga.edu/index.php/databases/spta-717-genome</ext-link>) presents only INRA 717-1B4 genomic regions with high similarity to the <italic>P. trichocarpa</italic> genomic reference sequences. We assembled draft genomic scaffolds by a combination of <italic>de novo</italic> assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4. In total, 419,969 scaffolds of length larger than 500 bp were generated. The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp. The N50 contig length is 3,850 bp when considering contigs larger than 1,000 bp. Probably due to the high level of heterozygosity of this interspecific hybrid, the accumulated scaffold length is with 0.9 GB about twice the expected size of the haploid nuclear genome. DNA sequences of the genomic scaffolds of INRA 717-1B4 are publicly available for Blast analyses and download via the new INRA web portal at <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/">https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/</ext-link>. This new genomic sequence resource will complement the already available INRA 717-1B4 resources and will facilitate the future optimization of genetic transformation experiments to discover gene function.</p></abstract>

Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome.jgi.doe.gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1.1 of sPta717 at http://aspendb.uga.edu/index.php/databases/spta-717-genome) presents only INRA 717-1B4 genomic regions with high similarity to the P. trichocarpa genomic reference sequences. We assembled draft genomic scaffolds by a combination of de novo assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4. In total, 419,969 scaffolds of length larger than 500 bp were generated. The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp. The N50 contig length is 3,850 bp when considering contigs larger than 1,000 bp. Probably due to the high level of heterozygosity of this interspecific hybrid, the accumulated scaffold length is with 0.9 GB about twice the expected size of the haploid nuclear genome. DNA sequences of the genomic scaffolds of INRA 717-1B4 are publicly available for Blast analyses and download via the new INRA web portal at https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/. This new genomic sequence resource will complement the already available INRA 717-1B4 resources and will facilitate the future optimization of genetic transformation experiments to discover gene function.

Whole-genome draft assembly of <italic>Populus tremula</italic> x <italic>P. alba</italic> clone INRA 717-1B4

EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry,

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Whole-genome draft assembly of  x  clone INRA 717-1B4

Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to...

Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Online veröffentlicht: 27. Okt. 2017

Seitenbereich: 74 - 79

DOI: https://doi.org/10.1515/sg-2016-0019

Schlüsselwörter
INRA 717-1B4, P. x canescens, poplars, next generation sequencing, genome assembly, scaffolds, model tree

© 2016 Malte Mader et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Online veröffentlicht: 27. Okt. 2017

Seitenbereich: 74 - 79

DOI: https://doi.org/10.1515/sg-2016-0019

SchlüsselwörterINRA 717-1B4, P. x canescens, poplars, next generation sequencing, genome assembly, scaffolds, model tree

© 2016 Malte Mader et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Schlüsselwörter
INRA 717-1B4, P. x canescens, poplars, next generation sequencing, genome assembly, scaffolds, model tree