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A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

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dc.contributor.author Palmada Flores, Marc
dc.contributor.author Orkin, Joseph D.
dc.contributor.author Haase, Bettina
dc.contributor.author Mountcastle, Jacquelyn
dc.contributor.author Bertelsen, Mads F.
dc.contributor.author Fedrigo, Olivier
dc.contributor.author Kuderna, Lukas, 1989-
dc.contributor.author Jarvis, Erich D.
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.date.accessioned 2022-05-04T06:38:57Z
dc.date.available 2022-05-04T06:38:57Z
dc.date.issued 2022
dc.identifier.citation Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience. 2022 Apr 1;11:giac026. DOI: 10.1093/gigascience/giac026
dc.identifier.issn 2047-217X
dc.identifier.uri http://hdl.handle.net/10230/52972
dc.description.abstract Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
dc.description.sponsorship The project that gave rise to these results received the support of 2 fellowships from "la Caixa" Foundation (ID 100010434) and from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847648. The fellowship codes are LCF/BQ/PI20/11760004 and LCF/BQ/DR20/11790032. T.M.B. is supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu,” funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, NIH 1R01HG010898-01A1, and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Gigascience. 2022 Apr 1;11:giac026
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.uri https://creativecommons.org/licenses/by/4.0/
dc.title A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/gigascience/giac026
dc.subject.keyword ALUs
dc.subject.keyword Strepsirrhine
dc.subject.keyword Lemuridae
dc.subject.keyword Long-read assembly
dc.subject.keyword Mitogenome
dc.subject.keyword Primate
dc.subject.keyword Repeats
dc.subject.keyword Scaffolding
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/847648
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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