TY - JOUR

T1 - A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

AU - Palmada-Flores, Marc

AU - Orkin, Joseph D.

AU - Haase, Bettina

AU - Mountcastle, Jacquelyn

AU - Bertelsen, Mads F.

AU - Fedrigo, Olivier

AU - Kuderna, Lukas F.K.

AU - Jarvis, Erich D.

AU - Marques-Bonet, Tomas

N1 - Publisher Copyright: © 2022 The Author(s). Published by Oxford University Press GigaScience.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - ALUs

KW - lemuridae

KW - long-read assembly

KW - mitogenome

KW - primate

KW - repeats

KW - scaffolding

KW - Strepsirrhine

U2 - 10.1093/gigascience/giac026

DO - 10.1093/gigascience/giac026

M3 - Journal article

C2 - 35365833

AN - SCOPUS:85127397244

VL - 11

JO - GigaScience

JF - GigaScience

SN - 2047-217X

M1 - giac026

ER -