A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)
Palmada-Flores, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Orkin, Joseph (Université de Montréal. Département d'anthropologie)
Haase, Bettina (The Rockefeller University. Vertebrate Genome Lab (USA))
Mountcastle, Jacquelyn (The Rockefeller University. Vertebrate Genome Lab (USA))
Bertelsen, Mads (University of Copenhagen. Department of Veterinary and Animal Sciences)
Fedrigo, Olivier (The Rockefeller University. Vertebrate Genome Lab (USA))
Kuderna, Lukas (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Jarvis, Erich (The Rockefeller University. Vertebrate Genome Lab (USA))
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)

Date:	2022
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.
Grants:	European Commission 847648 European Commission 864203 Agencia Estatal de Investigación BFU2017-86471-P Agencia Estatal de Investigación CEX2018-000792-M Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-880
Note:	Altres ajuts: "la Caixa" Foundation (ID 100010434)
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Strepsirrhine ; Primate ; Long-read assembly ; ALUs ; Repeats ; Lemuridae ; Mitogenome ; Scaffolding
Published in:	GigaScience, Vol. 11, Num. 1 (April 2022) , art. giac026, ISSN 2047-217X

DOI: 10.1093/gigascience/giac026
PMID: 35365833

7 p, 1.5 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > Institut Català de Paleontologia Miquel Crusafont (ICP)
Articles > Research articles
Articles > Published articles