DOI: 10.5061/dryad.k3j9kd5gx
title: De novo genome assembly for Eulemur rufifrons

description: As one of the most threatened mammalian taxa, lemurs of Madagascar are
 facing unprecedented anthropogenic pressures. To address conservation
 imperatives such as this, researchers have increasingly relied on
 conservation genomics to identify populations of particular concern.
 However, many of these genomic approaches necessitate high-quality
 genomes. While the advent of next generation sequencing technologies and
 the resulting reduction of associated costs have led to the proliferation
 of genomic data and high-quality reference genomes, global discrepancies
 in genomic sequencing capabilities often result in biological samples from
 biodiverse host countries being exported to facilities in the Global
 North, creating inequalities in access and training within genomic
 research. Here, we present the first reference genome for the endangered
 red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts
 conducted entirely within the host country using portable Oxford Nanopore
 sequencing. Using an archived E. rufifrons specimen, we conducted
 long-read, nanopore sequencing at the Centre ValBio Research Station near
 Ranomafana National Park, in rural Madagascar, generating over 750 Gb of
 sequencing data from 10 MinION flow cells. Exclusively using this
 long-read data, we assembled 2.215 gigabase, 20,330-contig assembly with
 an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x
 average coverage and was comparable in completeness to other primate
 reference genomes, with a 95.51% BUSCO completeness score for
 primate-specific genes. As the first reference genome for E. rufifrons and
 the only annotated genome available for the speciose Eulemur genus, this
 resource will prove vital for conservation genomic studies while our
 efforts exhibit the potential of this protocol to address research
 inequalities and build genomic capacity. 
description: To conduct whole genome sequencing within Madagascar, we
 extracted DNA from tissue (skin and spleen) of an archived Eulemur
 rufifrons specimen that was opportunistically collected within Ranomafana
 National Park and stored at -20 ºC at the nearby Centre ValBio Research
 Station. Genomic library preparation was conducted with Field Sequencing
 Kit (Oxford Nanopore SQK-LRK001) and Ligation Sequencing kit (Oxford
 Nanopore SQK-LSK109). All genomic sequencing was conducted within
 Madagascar at the Centre ValBio Research Station on portable MinION
 sequencers (Mk1C and Mk1B; Oxford Nanopore Technologies). All
 bioinformatic analyses to clean and assemble the genome were performed on
 the Rutgers Amarel high performance computing (HPC) cluster. The
 bioinformatic pipline rebasecalled reads with Dorado (0.3.4) before using
 the Flye (2.9.1) for assembly and Medaka (1.9.1) for polishing.
 Contaminants were removed with Kraken2 (2.1.3), repetive regions masked
 with RepeatMasker (4.1.5), and scaffolding was performed with RagTag
 (2.1.0).
description: # De novo genome assembly for Eulemur rufifrons
 [https://doi.org/10.5061/dryad.k3j9kd5gx](https://doi.org/10.5061/dryad.k3j9kd5gx) ## Description of the data and file structure Data for "De novo genome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar", a resource for conservation and evolutionary genomics studies.  **eulemur_rufifrons_wgs_renamed.fasta** ## Code/Software All scripts used for bioinformatic analyses are available at [[https://github.com/lhauff/Eulemur_genome_assembly.git](https://github.com/lhauff/Eulemur_genome_assembly.git)] ([https://github.com/lhauff/Eulemur_genome_assembly.git](https://github.com/lhauff/Eulemur_genome_assembly.git))