An Improved Chromosome-scale Genome Assembly and Population Genetics resource forPopulus tremula
Authors: Robinson Kathryn M. , Schiffthaler Bastian , Liu Hui , Westman Sara M. , Rendón-Anaya Martha , Kalman Teitur Ahlgren , Kumar Vikash , Canovi Camilla , Bernhardsson Carolina , Delhomme Nicolas , Jenkins Jerry , Wang Jing , Mähler Niklas , Richau Kerstin H. , Stokes Victoria , A’Hara Stuart , Cottrell Joan , Coeck Kizi , Diels Tim , Vandepoele Klaas , Mannapperuma Chanaka , Park Eung-Jun , Plaisance Stephane , Jansson Stefan , Ingvarsson Pär K. , Street Nathaniel R. 
Published: October 2019

AbstractAspen (Populus tremulaL.) is a widely distributed keystone species and a model system for forest tree genomics, with extensive resources developed for population genetics and genomics. Here we present an updated resource comprising a chromosome-scale assembly ofP. tremulaand population genetics and genomics data integrated into thePlantGenIE.orgweb resource. We demonstrate use of the diverse data types included to explore the genetic basis of natural variation in leaf size and shape as examples of traits with complex genetic architecture.We present a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts from 37,184 gene loci. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly, the UmAsp re-sequencing data and existing whole genome re-sequencing data from the Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections to perform genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network (AspLeaf, available inPlantGenIE.org), which we further used to explore the functions of candidate genes identified from the GWAS.We examined synteny to the referenceP. trichocarpaassembly and identifiedP. tremula-specific regions. Analysis of whole-genome duplication indicated differential substitution rates for the twoPopulusspecies, indicating more rapid evolution inP. tremula. A GWAS of 26 leaf physiognomy traits and all SNPs in each of the three aspen collections found significant associations for only two traits in ScotAsp collection and one in UmAsp, whereas subsetting SNPs to those in open chromatin regions revealed associations for a further four traits among all three aspen collections. The significant SNPs were associated with genes annotated for developmental and growth functions, which represent candidates for further study. Of particular interest was a 177-kbp region of chromosome 9 harbouring SNPs associated with multiple leaf phenotypes in ScotAsp, with the set of SNPs in linkage disequilibrium explaining 24 to 30 % of the phenotypic variation in leaf indent depth variation.We have incorporated the assembly, population genetics, genomics and leaf physiognomy GWAS data into thePlantGenIE.orgweb resource, including updating existing genomics data to the new genome version. This enables easy exploration and visualisation of the genomics data and exploration of GWAS results. We provide all raw and processed data used for the presented analyses to facilitate reuse in future studies.