The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

• Published in: PloS one Vol. 10; no. 9; pp. e0139075 - 12
• Main Authors: Belkorchia, Abdel, Gasc, Cyrielle, Polonais, Valérie, Parisot, Nicolas, Gallois, Nicolas, Ribière, Céline, Lerat, Emmanuelle, Gaspin, Christine, Pombert, Jean-François, Peyret, Pierre, Peyretaillade, Eric
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.09.2015; Public Library of Science (PLoS)
• Subjects: Algorithms; Annotations; Base Sequence; Bioinformatics; Biology; Computer applications; DNA sequencing; DNA, Intergenic - genetics; Encephalitozoon - genetics; Eukaryotes; Gene sequencing; Genes; Genes, Fungal - genetics; Genetic aspects; Genome Size; Genomes; Genomics; Life assessment; Life Sciences; Methods; Microsporidia; Molecular Sequence Annotation; Molecular Sequence Data; Nucleotide sequence; Open Reading Frames - genetics; Parasites; Phylogeny; Predictions; Proteins; Quantitative Methods; Reproducibility of Results; France; United States > US; Illinois
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0139075

The proper prediction of the gene catalogue of an organism is essential to obtain a representative snapshot of its overall lifestyle, especially when it is not amenable to culturing. Microsporidia are obligate intracellular, sometimes hard to culture, eukaryotic parasites known to infect members of every animal phylum. To date, sequencing and annotation of microsporidian genomes have revealed a poor gene complement with highly reduced gene sizes. In the present paper, we investigated whether such gene sizes may have induced biases for the methodologies used for genome annotation, with an emphasis on small coding sequence (CDS) gene prediction. Using better delineated intergenic regions from four Encephalitozoon genomes, we predicted de novo new small CDSs with sizes ranging from 78 to 255 bp (median 168) and corroborated these predictions by RACE-PCR experiments in Encephalitozoon cuniculi. Most of the newly found genes are present in other distantly related microsporidian species, suggesting their biological relevance. The present study provides a better framework for annotating microsporidian genomes and to train and evaluate new computational methods dedicated at detecting ultra-small genes in various organisms.