Improving genome assemblies and annotations for nonhuman primates

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

The study of nonhuman primates (NHP) is key to understanding human evolution, in addition to being an important model for biomedical research. NHPs are especially important for translational medicine. There are now exciting opportunities to greatly increase the utility of these models by incorporating Next Generation (NextGen) sequencing into study design. Unfortunately, the draft status of nonhuman genomes greatly constrains what can currently be accomplished with available technology. Although all genomes contain errors, draft assemblies and annotations contain so many mistakes that they make currently available nonhuman primate genomes misleading to investigators conducting evolutionary studies; and these genomes are of insufficient quality to serve as references for NextGen studies. Fortunately, NextGen sequencing can be used in the production of greatly improved genomes. Existing Sanger sequences can be supplemented with NextGen whole genome, and exomic genomic sequences to create new, more complete and correct assemblies. Additional physical mapping, and an incorporation of information about gene structure, can be used to improve assignment of scaffolds to chromosomes. In addition, mRNA-sequence data can be used to economically acquire transcriptome information, which can be used for annotation. Some highly polymorphic and complex regions, for example MHC class I and immunoglobulin loci, will require extra effort to properly assemble and annotate. However, for the vast majority of genes, a modest investment in money, and a somewhat greater investment in time, can greatly improve assemblies and annotations sufficient to produce true, reference grade nonhuman primate genomes. Such resources can reasonably be expected to transform nonhuman primate research.

Original languageEnglish (US)
Article numberilt037
Pages (from-to)144-153
Number of pages10
JournalILAR Journal
Volume54
Issue number2
DOIs
StatePublished - Nov 1 2013

Fingerprint

genome assembly
Primates
Genes
Genome
genome
Translational Medical Research
physical chromosome mapping
Immunoglobulin Isotypes
biomedical research
Transcriptome
transcriptome
immunoglobulins
Biomedical Research
medicine
Chromosomes
genes
experimental design
Scaffolds
Research Personnel
Medicine

Keywords

  • Ape, evolution
  • Genome annotation
  • Genome assembly
  • Lemur
  • Monkey
  • Nonhuman primates
  • Translational research

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Animal Science and Zoology

Cite this

Improving genome assemblies and annotations for nonhuman primates. / Norgren, Robert B.

In: ILAR Journal, Vol. 54, No. 2, ilt037, 01.11.2013, p. 144-153.

Research output: Contribution to journalArticle

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