A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>)
Stinging nettles (<i>Urtica dioica</i>) 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 <i>Urtica dioica</i>...
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MDPI AG
2025-01-01
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| author | Kaede Hirabayashi Christopher R. Dumigan Matúš Kučka Diana M. Percy Gea Guerriero Quentin Cronk Michael K. Deyholos Marco Todesco |
| author_facet | Kaede Hirabayashi Christopher R. Dumigan Matúš Kučka Diana M. Percy Gea Guerriero Quentin Cronk Michael K. Deyholos Marco Todesco |
| author_sort | Kaede Hirabayashi |
| collection | DOAJ |
| description | Stinging nettles (<i>Urtica dioica</i>) 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 <i>Urtica dioica</i> 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. |
| format | Article |
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| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-01-01 |
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| series | Plants |
| spelling | doaj-art-4a3d311b479e416ba3e04b7d06d6fbb02025-01-10T13:19:50ZengMDPI AGPlants2223-77472025-01-0114112410.3390/plants14010124A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>)Kaede Hirabayashi0Christopher R. Dumigan1Matúš Kučka2Diana M. Percy3Gea Guerriero4Quentin Cronk5Michael K. Deyholos6Marco Todesco7Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, CanadaBiology Department, University of British Columbia, 1177 Research Rd, Kelowna, BC V1V 2W9, CanadaBiology Department, University of British Columbia, 1177 Research Rd, Kelowna, BC V1V 2W9, CanadaBotany Department, University of British Columbia, Vancouver, BC V6T 1Z4, CanadaLuxembourg Institute of Science and Technology, Technology (LIST), 5, Rue Bommel, L-4940 Hautcharage, LuxembourgBotany Department, University of British Columbia, Vancouver, BC V6T 1Z4, CanadaBiology Department, University of British Columbia, 1177 Research Rd, Kelowna, BC V1V 2W9, CanadaMichael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, CanadaStinging nettles (<i>Urtica dioica</i>) 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 <i>Urtica dioica</i> 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.https://www.mdpi.com/2223-7747/14/1/124genome assembly<i>Urtica dioica</i>stinging nettletrichomesfiber cropschromosomal structural variation |
| spellingShingle | Kaede Hirabayashi Christopher R. Dumigan Matúš Kučka Diana M. Percy Gea Guerriero Quentin Cronk Michael K. Deyholos Marco Todesco A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) Plants genome assembly <i>Urtica dioica</i> stinging nettle trichomes fiber crops chromosomal structural variation |
| title | A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) |
| title_full | A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) |
| title_fullStr | A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) |
| title_full_unstemmed | A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) |
| title_short | A High-Quality Phased Genome Assembly of Stinging Nettle (<i>Urtica dioica</i> ssp. <i>dioica</i>) |
| title_sort | high quality phased genome assembly of stinging nettle i urtica dioica i ssp i dioica i |
| topic | genome assembly <i>Urtica dioica</i> stinging nettle trichomes fiber crops chromosomal structural variation |
| url | https://www.mdpi.com/2223-7747/14/1/124 |
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