35th NPS abstract book

P35
Population-scale characterisation of copy number variations in the gene
space of Picea glauca
A. SAHLI 1 , I. GIGUÈRE 1 , J. PRUNIER 1 , N. ISABEL 2 , J. BEAULIEU 1 , J. BOUSQUET 1 and J. MACKAY 1, 3
1 Center for Forest Research and Institute for Systems and Integrative Biology, Université Laval, 1030,
avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada; 2 Natural Resources Canada, Canadian
Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., Stn. Sainte-Foy, Quebec City, QC, G1V
4C7, Canada; 3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
3RB, UK
Copy number variations (CNVs) are large genetic variations present in the genome of every
multicellular organism examined so far. They are believed to play an important role in the evolution
and adaptation of species. In plants, little is known about the characteristics of CNVs. Here, we used
SNP-array intensity data for pedigrees and trees sampled from natural populations to scan the gene
space of Picea glauca for CNVs. We were particularly interested in the characterisation of CNVs
abundance, inheritance modalities, frequency spectrum and functional impact. Our findings
indicated that CNVs affect a small proportion of the gene space (less than 5%) and are
predominantly bi-allelic copy number losses. CNVs were found to follow the Mendelian inheritance
and many resulted from spontaneous mutations. The CNV frequency spectrum suggests that they
are mostly under purifying selection and that few genes may be under positive or balancing
selection. The functional annotation of CNV genes shows enrichment in genes involved in response
to environment, growth and development regulation processes. This study represents a first report
on CNVs in conifer trees at the genome and population scale and contributes to our understanding
of the genomic basis of evolution and population diversity in forest trees.
P36
Assembly challenges of the highly heterogeneous and repetitive genomes of
Populus tremula and Populus tremuloides
Y.-C. LIN, J. WANG, N. DELHOMME, B. SCHIFFTHALER, N. MÄHLER, D. SUNDELL, C.
MANNAPERUMA, K.M. ROBINSON, Y. VAN DE PEER, P. INGVERSSON, T.R. HVIDSTEN, S. JANSSON
and N.R. STREET
Department of Plant Physiology, Umeå University, Artedigränd 7, 90736 Umeå, Sweden; Department
of Biostatistics, Norwegian University of Life Sciences, Universitetstunet 3, 1432 Ås, Norway;
Department of Bioinformatics and Systems Biology, University of Ghent, Technologiepark 927, 9052
Ghent, Belgium
The European and American aspens, Populus tremula and Populus tremuloides, are ecological keystone and
scientific model forest tree species. Currently, most of the sequencing-based analyses of these species are
based on the genome assembly of the black cottonwood P. trichocarpa, a distant relative. This affects
alignment rates, especially for nongenic analyses. The aspen science community in particular, but also the
plant science community as a whole, would therefore benefit from genome assemblies of these two aspens.
These, currently undergoing, are challenging, as their genomes are highly heterozygous and repetitive, causing
extensive assembly fragmentation. Here, we first demonstrate the need for assemblies of P. tremula and P.
tremuloides by evaluating sequence alignment to the existing P. trichocarpa reference. We further present our
refined genome assembly strategies, leading to better assemblies of these two genomes. In parallel to this
genomic effort, we also present our de-novo transcriptome assembly of P. tremula, based on a comprehensive
RNA-Seq tissue catalog. Integrating these together, we assess the completeness of the genomes and their gene
spaces in our assemblies. This, ultimately, allows us to conduct a comparative genomics analysis that gives
insight into three members of the genus Populus, discussing their biological key differences and similarities.
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