title: The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes.
abstract: 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.
authors.affiliation: Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, F-63000, Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63171, Aubière, France.
authors.forename: Abdel
authors.initials: A
authors.lastname: Belkorchia
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Gasc
authors.affiliation: Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, F-63000, Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63171, Aubière, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Polonais
authors.affiliation: Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Gallois
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Ribière
authors.affiliation: Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lerat
authors.affiliation: INRA, UBIA UR 875, F-31320, Castanet-Tolosan, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.affiliation: Illinois Institute of Technology, Department of Biology, 3105 South Dearborn Street, Chicago, Illinois, 60616, United States of America.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Pombert
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001, Clermont-Ferrand, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
mesh_terms: D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics; D016819:Encephalitozoon / Q000235:genetics*; D005800:Genes, Fungal / Q000235:genetics*; D059646:Genome Size; D023281:Genomics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D015203:Reproducibility of Results
chemical_list: D021901:DNA, Intergenic