35th NPS abstract book

Comparative genomics of the quaking aspens
Populus tremula and P. tremuloides
S2.3
YAO-CHENG LIN 1 , NICOLAS DELHOMME 2 , JING WANG 3 , 16:15–16:45
BASTIAN SCHIFFTHALER 2 , MANFRED GRABHERR 4 , NEDA
ZAMANI 4 , MARC P HÖPNNER 4 , CHANAKA
MANNAPPERUMA 2 , NIKLAS MÄHLER 5 , DAVID SUNDELL 2 ,
YVES VAN DE PEER 1,6 , TORGEIR R HVIDSTEN 5 , STEFAN
JANSSON 2, PÄR K INGVARSSON 3 and NATHANIEL R
STREET 1
nathaniel.street@umu.se
1 Department of Plant Systems Biology (VIB) and Department of Plant
Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium;
2 Umeå Plant Science Centre, Department of Plant Physiology, Umeå
University, SE-907 81, Umeå, Sweden; 3 Umeå Plant Science Centre,
Department of Ecology and Environmental Science, Umeå University, SE-
901-97, Umeå, Sweden; 4 Department of Medical Biochemistry and
Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
5 Department of Chemistry, Biotechnology and Food Science, Norwegian
University of Life Sciences, 1432 Ås, Norway; 6 Genomics Research
Institute, University of Pretoria, Hatfield Campus, 0028 Pretoria, South
Africa
European and North American aspens, Populus tremula and P. tremuloides, are keystone species in
addition to being extensively used as model systems for forest tree research. To date, genomics
analyses in these species required use of the P. trichocarpa reference genome sequence. However,
this is often limiting due to poor sequence alignment rates. Given these limitations, we undertook
sequencing and assembly of the two aspen genomes in addition to re-sequencing 24 P. tremula and
22 P. tremuloides individuals and we are extending our sequencing to additional aspen species.
Analysis of kmer content and alignment of sequence reads to the P. trichocarpa reference revealed
rapid divergence of intergenic regions compared to the reference P. trichocarpa genome assembly in
addition to high rates of heterozygosity. We subsequently produced next generation sequencing
based de novo genome assemblies that were ab initio annotated. This resource allowed comparative
analysis to the reference assembly as well as among aspen species. To complement these analyses,
extensive RNA-Seq based transcript sequencing efforts were performed and used in combination
with large-scale transcriptomics studies at the Umeå Plant Science Centre. Whole genome alignment
and population level genotype data were used to identify regions of the aspen genome that have
rapidly diverged from the reference P. trichocarpa genome as well as to identify novel, aspen
specific features. We have focused on annotating and comparing both the protein coding and noncoding
gene space.
Assembling the aspen genome proved challenging as a result of extensive heterozygosity, driven by a
combination of both SNPs and INDELs, leading to frequent haplotype splitting. However, the gene
space is comprehensively represented, facilitating many comparative genomics analyses.
The developed resources have been integrated within the PlantGenIE.org web platform to allow the
wider community to benefit from and contribute to this genome project.
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