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

Malte Mader 1 , Marie-Christine Le Paslier 2 , Rémi Bounon 2 , Aurélie Bérard 2 , Patricia Faivre Rampant 2 , Matthias Fladung 1 , Jean-Charles Leplé 3 , 4 , and Birgit Kersten 1
  • 1 Thünen Institute of Forest Genetics, , Germany
  • 2 , France
  • 3 , 45075, Orléans, France
  • 4 BIOGECO, INRA, Université Bordeaux, 33610, France


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.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • Christe C, Stölting KN, Bresadola L, Fussi B, Heinze B, Wegmann D, Lexer C (2016) Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow. Mol Ecol 25 (11):2482-2498. http://dx.doi.org/10.1111/mec.13587

  • Dickmann D, Stuart KW (1993) The culture of poplars in eastern North America. Michigan: Michigan State University, 1st edition (1983), 168 p

  • Eckenwalder JE (1996) Systematics and evolution of Populus. In: Stettler RF, Bradshaw Jr. HD, Heilman PE, Hinckley TM (eds) Biology of Populus and its implications for management and conservation. Ottawa, Ontario, Canada: NRC Research Press, National Research Council of Canada, pp 7–32, ISBN 0660165066, 9780660165066

  • Fladung M, Altosaar I, Bartsch D, Baucher M, Boscaleri F, Gallardo F, Häggman H, Hoenicka H, Nielsen K, Paffetti D, Séguin A, Stotzky G, Vettori C (2012) European discussion forum on transgenic tree biosafety. Nature Biotechnology 30 (1): 37-38. http://dx.doi.org/10.1038/nbt.2078

  • Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QC (2015) Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol 24 (13):3243-3256. http://dx.doi.org/10.1111/mec.13126

  • Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29 (8):1072-1107. http://dx.doi.org/10.1093/bioinformatics/btt086

  • Jansson S, Douglas CJ (2007) Populus: A model system for plant biology. Annu Rev Plant Biol 58:435-458. http://dx.doi.org/10.1146/annurev.arplant.58.032806.103956

  • Kersten B, Faivre Rampant P, Mader M, Le Paslier MC, Bounon R, Berard A, Vettori C, Schroeder H, Leple JC, Fladung M (2016) Genome sequences of Populus tremula chloroplast and mitochondrion: Implications for holistic poplar breeding. PLoS One 11 (1):e0147209. http://dx.doi.org/10.1371/journal.pone.0147209

  • Kersten B, Pakull B, Fladung M (2017) Genomics of sex determination in dioecious trees and woody plants. Trees – Structure and Function 31 (4):1113–1125. http://dx.doi.org/10.1007/s00468-017-1525-7

  • Ky CL, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (2000) Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.). Theor Appl Genet 101 (4):669-676. http://dx.doi.org/10.1007/s001220051529

  • Lemoine M (1973) Amélioration des peupliers de la section Leuce sur sols hydromorphes [Thesis]: University of Nancy, France

  • Leplé JC, Brasileiro ACM, Michel MF, Delmotte F, Jouanin L (1992) Transgenic poplars: expression of chimeric genes using four different constructs. Plant Cell Rep 11:137-141. http://dx.doi.org/10.1007/BF00232166

  • Licht LA, Isebrands JG (2005) Linking phytoremediated pollutant removal to biomass economic opportunities. Biomass Bioenergy 28 (2):203-218. http://dx.doi.org/10.1016/j.biombioe.2004.08.015

  • Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, et al. (2013) Genomic insights into salt adaptation in a desert poplar. Nat Commun 4:2797. http://dx.doi.org/10.1038/ncomms3797

  • Pilate G, Dejardin A, Leple JC (2012) Chapter 1 - Field trials with lignin-modified transgenic trees. In: Lise J, Catherine L (eds) Advances in Botanical Research. Volume 61 (Lignins). London, Oxford, Boston, New York, San Diego: Academic Press, pp 1-36. ISBN 0124160239

  • Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, Le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, Morgante M (2016) Characterization of the poplar pan-genome by genome-wide identification of structural variation. Mol Biol Evol 33 (10):2706-2719. http://dx.doi.org/10.1093/molbev/msw161

  • Sjödin A, Street NR, Sandberg G, Gustafsson P, Jansson S (2009) The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome New Phytol 182 (4):1013-1025. http://dx.doi.org/10.1111/j.1469-8137.2009.02807.x

  • Slavov GT, Zhelev P (2010) Salient biological features, systematics, and genetic variation of Populus. In: Jansson S, Bhalerao R, Groover A (eds) Genetics and Genomics of Populus, Plant Genetics and Genomics: Crops and Models. Berlin, Heidelberg, New York: Springer, pp 15-38, ISBN 978-1-4419-1540-5 (Print) 978-1-4419-1541-2 (Online)

  • Stanton BJ, Neale DB, Li S (2010) Populus breeding: From the classical to the genomic approach. In: Jansson S, Bhalerao R, Groover A (eds) Genetics and Genomics of Populus. Dordrecht, Netherlands: Springer Science+Business Media, pp 309-348

  • Stettler RF, Bradshaw Jr. HD, Heilman PE, Hinckley TM (1996) Biology of Populus and its implications for management and conservation. Ottawa, Ontario, Canada: NRC Research Press, National Research Council of Canada, 539 p, ISBN 0660165066, 9780660165066

  • Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313 (5793):1596-1604. http://dx.doi.org/10.1126/science.1128691

  • Walle IV, Van Camp N, Van de Casteele L, Verheyen K, Lemeur R (2007) Short-rotation forestry of birch, maple, poplar and willow in Flanders (Belgium) II. Energy production and CO2 emission reduction potential. Biomass Bioenergy 31 (5):276-283. http://dx.doi.org/10.1016/j.biombioe.2007.01.019

  • Walter C, Fladung M, Boerjan W (2010) The 20-year environmental safety record of GM trees. Nat Biotechnol 28 (7):656-658. http://dx.doi.org/10.1038/nbt0710-656

  • Wullschleger SD, Jansson S, Taylor G (2002) Genomics and forest biology: Populus emerges as the perennial favorite. Plant Cell 14 (11):2651-2655. http://dx.doi.org/10.1105/tpc.141120

  • Zhou X, Jacobs TB, Xue LJ, Harding SA, Tsai CJ (2015) Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate:CoA ligase specificity and redundancy. New Phytol 208 (2):298-301. http://dx.doi.org/10.1111/nph.13470


Journal + Issues