ABSTRACT
The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.
Subject(s)
Aspergillus nidulans/genetics , Fungal Proteins/genetics , Genes, Fungal , Genome, Fungal , Genomics , Aspergillus nidulans/physiologyABSTRACT
The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
Subject(s)
Genome, Bacterial , Metagenome/genetics , Sequence Analysis, DNA , Bacteria/classification , Bacteria/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biodiversity , Computational Biology , Databases, Genetic , Gastrointestinal Tract/microbiology , Genes, Bacterial , Genetic Variation , Genome, Archaeal , Humans , Metagenomics/methods , Metagenomics/standards , Mouth/microbiology , Peptides/chemistry , Peptides/genetics , Phylogeny , Respiratory System/microbiology , Sequence Analysis, DNA/standards , Skin/microbiology , Urogenital System/microbiologyABSTRACT
A report of the meeting Comparative Genomics of Eukaryotic Microorganisms, 17-22 October 2009, San Feliu de Guixols, Spain.