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High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species

Fleck, Steven1; Tomlin, Crystal1; Augusto da Silva Coelho, Flavio1; Richter, Michaela1; Danielson, Erik2; Backenstose, Nathan1; Krabbenhoft, Trevor1; Lindqvist, Charlotte1; Albert, Victor1

Research facility: University at Buffalo, State University of New York
Published Dec 18, 2023 on Dryad. https://doi.org/10.5061/dryad.7sqv9s4xh

Data files

Dec 18, 2023 version files 14.54 GB

Abstract

With populations of threatened and endangered species declining worldwide, efforts are being made to generate high-quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high-quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a whole genome triplication at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.