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.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.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.doi http://dx.doi.org/10.1093/dnares/dsac013
- dc.identifier.issn 1340-2838
- dc.identifier.uri http://hdl.handle.net/10230/53524
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CGL2017-83407-P
- 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.accessRights info:eu-repo/semantics/openAccess
- 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.type.version info:eu-repo/semantics/publishedVersion