First Assembly of a Draft Genome of the Critically Endangered Northern Muriqui ( Brachyteles hypoxanthus , Primates, Atelidae) Including Non‐Invasive Genotyping Strategies for the Species

Authors

Amanda Alves de Melo-Ximenes
Romina Batista
Leonardo Carlos Jeronimo Corvalán
Tomas Marques-Bonet
Lukas Kuderna
Kyle Farh
Jeffrey Rogers
Mariane da Cruz Kaizer
Jean Philippe Boubli
Fabiano Rodrigues de Melo
Rhewter Nunes
Mariana Pires de Campos Telles

Language

English

Publication Date

8-1-2025

Journal

Ecology and Evolution

DOI

10.1002/ece3.71356

PMID

40843033

PMCID

PMC12365342

PubMedCentral® Posted Date

8-19-2025

PubMedCentral® Full Text Version

Post-print

Abstract

Genomic resources, such as draft genomes, are vital for biodiversity monitoring and conservation. For endangered species, they enable the development of tools like organellar genomes and molecular markers, which are crucial for population genetics. Advances in sequencing technologies now allow high‐throughput genotyping with detailed amplicon sequences, enhancing genetic variation studies. The northern muriqui ( Brachyteles hypoxanthus ), a critically endangered primate endemic to Brazil's Atlantic Forest, currently lacks both nuclear and mitochondrial genome data and species‐specific microsatellite markers for population genetic studies. We assembled a 2.52 Gb draft genome for B. hypoxanthus with 202,243 contigs (N50 = 29,134 bp), and BUSCO analyses indicated 52% completeness and 15.5% fragmented genes. The complete 16,635 bp mitochondrial genome retains the conserved mammalian structure with 22 tRNAs, 2 rRNAs, 13 CDS, and an origin of replication. Additionally, we designed 31 SSR primer pairs suitable for non‐invasive sampling and genotyping, alongside two mtDNA and two sex‐determination primers, configured into three multiplex PCR sets. These genomic resources, including the draft genome, complete mitochondrial genome, and microsatellite markers, provide essential tools for evolutionary analyses and the genetic monitoring of B. hypoxanthus populations, supporting its conservation.

Keywords

conservation genomics, GBS, genomics, HTS, SSR, SSR‐Seq

Published Open-Access

yes

Recommended Citation

de Melo-Ximenes, Amanda Alves; Batista, Romina; Corvalán, Leonardo Carlos Jeronimo; et al., "First Assembly of a Draft Genome of the Critically Endangered Northern Muriqui ( Brachyteles hypoxanthus , Primates, Atelidae) Including Non‐Invasive Genotyping Strategies for the Species" (2025). Faculty and Staff Publications. 5083.
https://digitalcommons.library.tmc.edu/baylor_docs/5083