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. ..., 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 w..., , # 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))