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. 2024 Sep-Oct;176(5):e14511.
doi: 10.1111/ppl.14511.

An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula

Kathryn M Robinson #  1 , Bastian Schiffthaler #  1 , Hui Liu  2 , Sara M Rydman  1 , Martha Rendón-Anaya  3 , Teitur Ahlgren Kalman  1 , Vikash Kumar  1 , Camilla Canovi  1 , Carolina Bernhardsson  4 , Nicolas Delhomme  5 , Jerry Jenkins  6 , Jing Wang  7 , Niklas Mähler  1 , Kerstin H Richau  1 , Victoria Stokes  8 , Stuart A'Hara  8 , Joan Cottrell  8 , Kizi Coeck  9 , Tim Diels  10   11 , Klaas Vandepoele  10   11   12 , Chanaka Mannapperuma  1 , Eung-Jun Park  13 , Stephane Plaisance  9 , Stefan Jansson  1 , Pär K Ingvarsson  3 , Nathaniel R Street  1   14
Affiliations

An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula

Kathryn M Robinson et al. Physiol Plant. 2024 Sep-Oct.

Erratum in

Abstract

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

Keywords: ATAC‐Seq; GWAS; Populus; aspen; co‐expression; genetic architecture; genome assembly; leaf physiognomy; leaf shape; leaf size; lncRNA; natural selection; population genetics.

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References

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