De novo genome assembly for Eulemur rufifrons
Data files
May 15, 2024 version files 2.25 GB
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eulemur_rufifrons_wgs_renamed.fasta
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README.md
Aug 12, 2024 version files 2.30 GB
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eulemur_rufifrons_mitogenome.bed
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eulemur_rufifrons_prot.fasta
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eulemur_rufifrons_wgs_final.fasta
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README.md
Abstract
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.
README: De novo genome assembly for Eulemur rufifrons
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
Methods
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).