Dataset Information

Improving genome assemblies and annotations for nonhuman primates.

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.

SUBMITTER: Norgren RB

PROVIDER: S-EPMC3814395 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Improving genome assemblies and annotations for nonhuman primates.

Norgren Robert B RB

ILAR journal 20130101 2

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 ...[more]

PMID: 24174438

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Project description:BACKGROUND:In terms of structure and function, the skull is one of the most complicated organs in the body. It is also one of the most important parts in terms of developmental and evolutionary origins. This complexity makes it difficult to obtain evolutionary assessments if, as is usually the case with fossils, only part of the skull is available. For this reason this study involves a set of comparisons whereby the smallest functional units are studied first, and these built up, through a triple-nested hierarchical design, into more complex anatomical regions and eventually into the skull-as-a-whole. This design has been applied to macaques (Macaca) in order to reveal patterns of variation at the different levels. The profiles of such variation have been obtained both within and between species. This has lead to a search for the skull parts that have undergone similar selection pressures during evolution and comparable development patterns in both ontogeny and phylogeny. RESULTS:Morphometric analysis (Principal Components) was used to obtain these profiles of species and sex separations based on 77 cranial variables from 11 species of macaques. The results showed that 7 functional units could be aggregated into three functionally reasonable anatomical regions on the basis of similarities in profiles. These were: the masticatory apparatus containing mandible, lower teeth and upper teeth, the face as a whole combining maxilla (actually lower face) and upper face, and the cranium as a whole involving cranium and calvaria. Twenty-six variables were finally selected for analyzing the morphology of the whole skull. This last showed an overall profile similar to that revealed in the masticatory apparatus but also contained additional information pertaining to individual species and species-groups separations. CONCLUSIONS:The study provides a model for carrying out analysis of species separations and sex variation simultaneously. Through this design it seems possible to see cranio-dental elements that may result from similar developmental processes, have similar functional adaptations, and show an appropriately integrated structure morphologically. This study also implies that the biological information drawn from part of skull alone, e.g. as in studies of incomplete fossils may provide misleading information.

Dataset Information

Improving genome assemblies and annotations for nonhuman primates.

Publications

Improving genome assemblies and annotations for nonhuman primates.

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