A new rhesus macaque assembly and annotation for next-generation sequencing analyses

Area of Science:

• Genomics
• Primate research
• Bioinformatics

Background:

• The rhesus macaque is vital for biomedical research, but existing genome assemblies (rheMac2, CR_1.0) have limitations.
• Gaps, errors, and fragmentation in current assemblies hinder accurate genomic analyses.
• High-quality genome data is essential for expression, genetic, and evolutionary studies.

Purpose of the Study:

• To develop a novel, high-quality de novo genome assembly and annotation for the rhesus macaque.
• To improve upon existing rhesus macaque genome assemblies (rheMac2, CR_1.0) in terms of completeness and accuracy.
• To provide a reliable genomic resource for next-generation sequencing studies.

Main Methods:

• Integrated Sanger and Illumina sequencing data for a new de novo assembly (MacaM).
• Incorporated mapping data and preliminary scaffold annotation for chromosome assembly.
• Assembled messenger RNA sequences from multiple tissues to identify complete proteins and genes.

Main Results:

• The MacaM assembly features a contig N50 size of 64 kb, more than double rheMac2 and nearly five times CR_1.0.
• MacaM demonstrates superior completeness and accuracy compared to rheMac2 and CR_1.0 based on Ion Torrent read alignments.
• Identified 11,712 complete proteins (9,524 genes) and annotated 18,757 transcripts (16,050 genes) with coding sequences.

Conclusions:

• The MacaM assembly and annotation provide a significantly improved representation of the rhesus macaque genome.
• This new resource enhances accuracy for next-generation sequencing studies, including RNA sequencing.
• MacaM will advance nonhuman primate research by offering a robust genomic foundation.