title: From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.
abstract: The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention.
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Misas
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia.
authors.forename: José Fernando
authors.initials: JF
authors.lastname: Muñoz
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia.
authors.forename: Juan Esteban
authors.initials: JE
authors.lastname: Gallo
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia.
authors.forename: Juan Guillermo
authors.initials: JG
authors.lastname: McEwen
authors.affiliation: Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia. Electronic address: oliver.clay@gmail.com.
authors.forename: Oliver Keatinge
authors.initials: OK
authors.lastname: Clay
mesh_terms: D016681:Genome, Fungal; D008928:Mitochondria / Q000378:metabolism*
keywords: DNA secondary structure; Fungal mitochondria; Genome assembly; Next generation sequencing; Repetitive DNA