Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

Abstract

The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference genome which until now was unavailable forA. f. fusciceps. The present study reports the first whole genome sequence and assembly ofA. f. fuscicepsgenerated using Oxford Nanopore long reads. DNA was extracted from a subadult male and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable to other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.

De novogenome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

“…Although some challenges were encountered while conducting sequencing in a remote region, such as expiration of consumables perhaps due to the tropical environment, our protocol proved to be adaptable and robust. This work joins the growing body of literature that showcase the technological advancements of portable, long-read sequencing technologies and associated bioinformatic processes that enable the creation and curation of reference genomes for species of conservation concern (e.g., Flack et al, 2023;Pozo et al, 2024).…”

“…In addition to being able to conduct rapid, in situ biodiversity assessments to confirm the presence of vulnerable Danfoss' mouse lemur (Microcebus danfossi), one research team was able to use their mobile genetics laboratories to provide a collaborative molecular workshop for local Malagasy students, who previously lacked of access to equipment and hands-on training as major barriers to pursuing such research (Blanco et al, 2020). Usage of portable ONT sequencing has also produced nanopore-only reference assemblies (e.g., Flack et al, 2023;Pozo et al, 2024), highlighting its potential to generate valuable genomic resources while providing underrepresented researchers pivotal access and training to molecular techniques.…”