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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; 11:6562532. [PMID: 35365833 PMCID: PMC8975718 DOI: 10.1093/gigascience/giac026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 02/19/2022] [Indexed: 01/31/2023] Open
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.
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Affiliation(s)
- Marc Palmada-Flores
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Joseph D Orkin
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Département d'anthropologie, Université de Montréal, Montréal, QC H3T 1N8, Canada
| | - Bettina Haase
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | | | - Mads F Bertelsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | - Lukas F K Kuderna
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Erich D Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Laboratory of Neurogenetics of Language, The Rockefeller University, NY 10065, USA
| | - Tomas Marques-Bonet
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelon 08028a, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
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