De novo whole-genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides)

Abstract

The southern muriqui (Brachyteles arachnoides) is one of the 2 species of muriquis (genus Brachyteles), the largest body-sized nonhuman primate from the Neotropics. Deforestation and illegal hunting have led to a continuing decline in the muriqui population, leading to their current classification as critically endangered. The lack of a reference genome for the genus Brachyteles prevents scientists from taking full advantage of genomic tools to improve their conservation status. This study reports the first whole-genome assemblies of the genus Brachyteles, using DNA from 2 zoo-housed southern muriqui females. We performed sequencing with Oxford Nanopore Technologies’ PromethION 2 Solo using a native DNA library preparation to preserve DNA modifications. We used Flye to assemble genomes for each individual. The best final assembly was 2.6 Gb, in 319 contigs, with an N50 of 58.8 Mb and an L50 of 17. BUSCO completeness score for this assembly was 99.5%. The assembly of the second individual had similar quality, with a length of 2.6 Gb, 759 contigs, an N50 of 47.9 Mb, an L50 of 18, and a BUSCO completeness score of 99.04%. Both assemblies had <1% duplicates, missing, or fragments. Gene model mapper detected 24,353 protein-coding genes, and repetitive elements accounted for 46% of the genome. We also reported the mitogenome, which had 16,562 bp over 37 genes, and global methylation of CpG sites, which revealed a mean of 80% methylation. Our study provides a high-quality reference genome assembly for the southern muriqui, expanding the tools that can be used to aid in their conservation efforts.