A High-Quality Phased Genome Assembly of Stinging Nettle (Urtica dioica ssp. dioica)
department or school: Science, Faculty of
department or school: Science, Irving K. Barber Faculty of (Okanagan)
department or school: Non UBC
department or school: Biology, Department of (Okanagan)
department or school: Botany, Department of
data provider: DSpace
identifier citation: Plants 14 (1): 124 (2025)
contributor: Michael Smith Laboratories
contributor: University of British Columbia. Biodiversity Research Centre
contributor: Beaty Biodiversity Museum
creator: Hirabayashi, Kaede
creator: Dumigan, Christopher R.
creator: Kučka, Matúš
creator: Percy, Diana M.
creator: Guerriero, Gea
creator: Cronk, Quentin C. B.
creator: Deyholos, Michael K.
creator: Todesco, Marco
issued: 2025-01-20T19:13:10Z
issued: 2025-01-03
description: Stinging nettles (Urtica dioica) have a long history of association with human civilization, having been used as a source of textile fibers, food and medicine. Here, we present a chromosome-level, phased genome assembly for a diploid female clone of Urtica dioica from Romania. Using a combination of PacBio HiFi, Oxford Nanopore, and Illumina sequencing, as well as Hi-C long-range interaction data (using a novel Hi-C protocol presented here), we assembled two haplotypes of 574.9 Mbp (contig N50 = 10.9 Mbp, scaffold N50 = 44.0 Mbp) and 521.2 Mbp (contig N50 = 13.5 Mbp, scaffold N50 = 48.0 Mbp), with assembly BUSCO scores of 92.6% and 92.2%. We annotated 20,333 and 20,140 genes for each haplotype, covering over 90% of the complete BUSCO genes and including two copies of a gene putatively encoding the neurotoxic peptide urthionin, which could contribute to nettle’s characteristic sting. Despite its relatively small size, the nettle genome displays very high levels of repetitiveness, with transposable elements comprising more than 60% of the genome, as well as considerable structural variation. This genome assembly represents an important resource for the nettle community and will enable the investigation of the genetic basis of the many interesting characteristics of this species.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/90148
note: Academic Editors: Françoise Martzand Michel ChalotReceived: 21 November 2024Revised: 24 December 2024Accepted: 2 January 2025Published: 3 January 2025Citation: Hirabayashi, K.;Dumigan, C.R.; Kucˇka, M.;Percy, D.M.; Guerriero, G.; Cronk, Q.;Deyholos, M.K.; Todesco, M.A High-Quality Phased GenomeAssembly of Stinging Nettle (Urticadioica ssp. dioica). Plants 2025, 14, 124.https://doi.org/10.3390/plants14010124Copyright: © 2025 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license(https://creativecommons.org/licenses/by/4.0/).ArticleA High-Quality Phased Genome Assembly of Stinging Nettle(Urtica dioica ssp. dioica)Kaede Hirabayashi 1 , Christopher R. Dumigan 2 , Matúš Kucˇka 2,3 , Diana M. Percy 4,5 , Gea Guerriero 6 ,Quentin Cronk 4,5,7 , Michael K. Deyholos 2 and Marco Todesco 1,2,4,5,*1 Michael Smith Laboratories, University of British Columbia, 2185 East Mall,Vancouver, BC V6T 1Z4, Canada; kaede.hirabayashi@msl.ubc.ca2 Biology Department, University of British Columbia, 1177 Research Rd, Kelowna, BC V1V 2W9, Canada;cdumigan94@gmail.com (C.R.D.); matkucka@gmail.com (M.K.); michael.deyholos@ubc.ca (M.K.D.)3 Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources,Slovak University of Agriculture in Nitra, 949 76 Nitra, Slovakia4 Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;diana.percy@botany.ubc.ca (D.M.P.); quentin.cronk@ubc.ca (Q.C.)5 Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada6 Luxembourg Institute of Science and Technology, Technology (LIST), 5, Rue Bommel,L-4940 Hautcharage, Luxembourg; gea.guerriero@list.lu7 Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC V6T 1Z4, Canada* Correspondence: mtodesco@msl.ubc.caAbstract: Stinging nettles (Urtica dioica) have a long history of association with humanciviliz…
has type: Article
is shown at: 10.14288/1.0447785
language: eng
peer review status: Reviewed
provider: Vancouver : University of British Columbia Library
publisher: Multidisciplinary Digital Publishing Institute
publisher DOI: 10.3390/plants14010124
rights: CC BY 4.0
rights URI: https://creativecommons.org/licenses/by/4.0/
scholar level: Faculty
scholar level: Researcher
subject: genome assembly
subject: Urtica dioica
subject: stinging nettle
subject: trichomes
subject: fiber crops
subject: chromosomal structural variation
subject: Hi-C protocol
type: Text
identifier URI: http://hdl.handle.net/2429/90148