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Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad

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dc.contributor.author Liedtke, H. Christoph
dc.contributor.author Cruz, Fernando
dc.contributor.author Gómez Garrido, Jèssica
dc.contributor.author Fuentes Palacios, Diego
dc.contributor.author Marcet Houben, Marina
dc.contributor.author Gut, Marta
dc.contributor.author Alioto, Tyler
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Gomez-Mestre, Ivan
dc.date.accessioned 2022-06-17T10:42:56Z
dc.date.available 2022-06-17T10:42:56Z
dc.date.issued 2022
dc.identifier.citation Liedtke HC, Cruz F, Gómez-Garrido J, Fuentes Palacios D, Marcet-Houben M, Gut M et al. Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad.
dc.identifier.issn 1340-2838
dc.identifier.uri http://hdl.handle.net/10230/53524
dc.description.abstract Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.
dc.description.sponsorship This research was funded by Plan Nacional I + D grant #CGL2017-83407-P awarded to I.G.-M. and a Ministerio de Ciencia e Innovación fellowship #IJC2018-035780-I awarded to H.C.L. TG’s group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); and from the European Union’s Horizon 2020 research and innovation programme (ERC-2016-724173)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.rights © Hans Christoph Liedtke et al 2022. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject.other Genòmica
dc.subject.other Amfibis
dc.title Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/dnares/dsac013
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CGL2017-83407-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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