De novo genome assembly for Eulemur rufifrons

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.