title: Genes in Hiding.
abstract: Unrecognizable genes are an unsettling problem in genomics. Here, we survey the various types of cryptic genes and the corresponding deciphering strategies employed by cells. Encryption that renders genes substantially different from homologs in other species includes sequence substitution, insertion, deletion, fragmentation plus scrambling, and invasion by mobile genetic elements. Cells decode cryptic genes at the DNA, RNA or protein level. We will focus on a recently discovered case of unparalleled encryption involving massive gene fragmentation and nucleotide deletions and substitutions, occurring in the mitochondrial genome of a poorly understood protist group, the diplonemids. This example illustrates that comprehensive gene detection requires not only auxiliary sequence information - transcriptome and proteome data - but also knowledge about a cell's deciphering arsenal.
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada. Electronic address: gertraud.burger@umontreal.ca.
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Moreira
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada.
authors.forename: Matus
authors.initials: M
authors.lastname: Valach
mesh_terms: D004272:DNA, Mitochondrial / Q000235:genetics; D056898:Euglenozoa / Q000235:genetics; D054629:Genome, Mitochondrial; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics; D017393:RNA Editing / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D004272:DNA, Mitochondrial
keywords: RNA editing; cryptic genes; diplonemids; gene fragmentation; multipartite mitochondrial DNA (mtDNA); trans-splicing