Retrieval of long DNA reads from herbarium specimens.

Autor:	Quatela AS; Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden.; Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden., Cangren P; Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden., Jafari F; Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran.; Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran., Michel T; Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK., de Boer HJ; Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway., Oxelman B; Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden.; Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden.
Jazyk:	angličtina
Zdroj:	AoB PLANTS [AoB Plants] 2023 Nov 08; Vol. 15 (6), pp. plad074. Date of Electronic Publication: 2023 Nov 08 (Print Publication: 2023).
DOI:	10.1093/aobpla/plad074
Abstrakt:	High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups. Competing Interests: The authors declare that they have no competing interests. (© The Author(s) 2023. Published by Oxford University Press on behalf of the Annals of Botany Company.)
Databáze:	MEDLINE
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