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

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 ext...

Descripción completa

Detalles Bibliográficos
Autores: Liedtke, H. Christoph, Cruz, Fernando, Gómez-Garrido, Jèssica, Fuentes Palacios, D., Marcet-Houben, M., Gut, Marta, Alioto, Tyler S., Gabaldón, T., Gómez-Mestre, Iván
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/362292
Acceso en línea:http://hdl.handle.net/10261/362292
Access Level:acceso abierto
id ES_4e82d7f2fde1d15bbb5a6be63d2656b6
oai_identifier_str oai:digital.csic.es:10261/362292
network_acronym_str ES
network_name_str España
repository_id_str
spelling Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toadLiedtke, H. ChristophCruz, FernandoGómez-Garrido, JèssicaFuentes Palacios, D.Marcet-Houben, M.Gut, MartaAlioto, Tyler S.Gabaldón, T.Gómez-Mestre, IvánGenomic 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.Oxford University PressConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2024202420222024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/362292reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1093/dnares/dsac013Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3622922026-05-22T06:33:51Z
dc.title.none.fl_str_mv Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
title Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
spellingShingle Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
Liedtke, H. Christoph
title_short Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
title_full Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
title_fullStr Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
title_full_unstemmed Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
title_sort Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad
dc.creator.none.fl_str_mv Liedtke, H. Christoph
Cruz, Fernando
Gómez-Garrido, Jèssica
Fuentes Palacios, D.
Marcet-Houben, M.
Gut, Marta
Alioto, Tyler S.
Gabaldón, T.
Gómez-Mestre, Iván
author Liedtke, H. Christoph
author_facet Liedtke, H. Christoph
Cruz, Fernando
Gómez-Garrido, Jèssica
Fuentes Palacios, D.
Marcet-Houben, M.
Gut, Marta
Alioto, Tyler S.
Gabaldón, T.
Gómez-Mestre, Iván
author_role author
author2 Cruz, Fernando
Gómez-Garrido, Jèssica
Fuentes Palacios, D.
Marcet-Houben, M.
Gut, Marta
Alioto, Tyler S.
Gabaldón, T.
Gómez-Mestre, Iván
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description 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.
publishDate 2022
dc.date.none.fl_str_mv 2022
2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/362292
url http://hdl.handle.net/10261/362292
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1093/dnares/dsac013
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869407761267163136
score 15,81155

Similares en LA Referencia