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

Abstract

BackgroundThe rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses.ResultsWe report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies.ConclusionsThe MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates.ReviewersThis article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.

The genome of the vervet (Chlorocebus aethiops sabaeus)

“…To discern whether vervets also display more frequent smaller-scale rearrangements, we first conducted a comparative analysis of total interspersed repeats, then performed detailed comparisons of synteny between the vervet genome and those of human and rhesus macaque. Total transposable elements (TEs) occupy ∼48% of the vervet genome and are distributed in a pattern comparable to that observed in rhesus macaque (Zimin et al 2014) and human (Supplemental Tables S3-S6 specificity for catarrhines. The chromosomal distribution of selected TEs (SINEs, LINEs, LTRs, and DNA transposons) showed the highest total coverage (>50%) on the sex chromosomes and on CAE 6 and 28, and the lowest coverage (44%) on CAE 8.…”

“…As this highly repetitive chromosome was present in half the number of copies as the autosomes, and was assembled de novo, further investigations will be required to fully characterize Chromosome Y (Hughes et al 2012). Similarly, we expected the male vervet Chromosome X to be assembled in fewer bases when compared to the assembled female Chromosome X of rhesus macaque (Zimin et al 2014). Assembled sizes for the male vervet and female rhesus macaque X Chromosomes are 144 and 148 Mb with spanned gaps of 5445 and 4281, respectively, suggesting slightly lower overall sequence representation in the vervet (Supplemental Table S1).…”

“…S8). We then aligned the ungapped regions to a nonreference-derived rhesus macaque MHC (Daza-Vamenta et al 2004); we used these data because the MHC region of the rheMac7 reference (Zimin et al 2014) contains several errors due to the complex SDs that characterize the MHC of all rhesus macaques examined to date (Daza-Vamenta et al 2004;Watanabe et al 2007). When compared to the rhesus macaque single haploid MHC region (Daza-Vamenta et al 2004), the vervet displayed highly conserved synteny with only minor structural variation (Fig.…”

Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation

“…Raw paired-end reads for R. brelichi, R. strykeri, and R. avunculus as well as those published for R. roxellana 4 and M. mulatta 13 were aligned to the R. bieti assembled genome (Rb0) using BWA with default parameters 56 (Supplementary Note). We performed SNP calling using SAMtools 57 (Supplementary Note).…”

“…The repeat-masked scaffolds of the R. bieti genome with sequence lengths >100,000 bp, which accounted for 92.45% of the assembled genome, were aligned to the M. mulatta genome 13 , which contains 21 chromosomes, using MUMmer v3.0 (ref. 68).…”