Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies

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• dc.contributor.author Naranjo Ortiz, Miguel Ángel, 1989-
• dc.contributor.author Molina, Manuel
• dc.contributor.author Fuentes Palacios, Diego
• dc.contributor.author Mixão, Verónica
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.date.accessioned 2023-03-07T07:12:50Z
• dc.date.available 2023-03-07T07:12:50Z
• dc.date.issued 2022
• dc.description.abstract Background: Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, heterokaryosis, or extreme compositional biases can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a nonnegligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. Findings: Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of nonchanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. Conclusions: Our results show that 10 (28.57%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least for some lineages within the Fungi.
• dc.description.sponsorship Supported by the Spanish Ministry of Science and Innovation (grant PGC2018-099921-B-I00), cofounded by the European Regional Development Fund (ERDF); the Catalan Research Agency (AGAUR), SGR423; the European Union's Horizon 2020 research and innovation program (ERC-2016–724173); the Gordon and Betty Moore Foundation (grant GBMF9742); and the Instituto de Salud Carlos III (IMPACT grant IMP/00019 and CIBERINFEC CB21/13/00061-ISCIII-SGEFI/ERDF).
• dc.format.mimetype application/pdf
• dc.identifier.citation Naranjo-Ortiz MA, Molina M, Fuentes D, Mixão V, Gabaldón T. Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies. Gigascience. 2022 Oct 7;11:giac088. DOI: 10.1093/gigascience/giac088
• dc.identifier.doi http://dx.doi.org/10.1093/gigascience/giac088
• dc.identifier.issn 2047-217X
• dc.identifier.uri http://hdl.handle.net/10230/56068
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Gigascience. 2022 Oct 7;11:giac088
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-099921-B-I00
• dc.rights © The Author(s) 2022. Published by Oxford University Press GigaScience. 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.keyword Aneuploidy
• dc.subject.keyword Genome assembly
• dc.subject.keyword Heterozygosity
• dc.subject.keyword Hybridization
• dc.subject.keyword Polyploidy
• dc.title Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion