title: A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.
abstract: Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.
authors.forename: Dante
authors.initials: D
authors.lastname: Travisany
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.
authors.forename: María Paz
authors.initials: MP
authors.lastname: Cortés
authors.affiliation: Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Latorre
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.
authors.forename: Alex
authors.initials: A
authors.lastname: Di Genova
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile.
authors.forename: Marko
authors.initials: M
authors.lastname: Budinich
authors.affiliation: BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile.
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Bobadilla-Fazzini
authors.affiliation: BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile.
authors.forename: Pilar
authors.initials: P
authors.lastname: Parada
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile.
authors.forename: Mauricio
authors.initials: M
authors.lastname: González
authors.affiliation: Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile. Electronic address: amaass@dim.uchile.cl.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Maass
mesh_terms: D013856:Acidithiobacillus thiooxidans / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D000220:Adaptation, Biological; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D004361:Drug Tolerance; D004783:Environmental Microbiology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007218:Industrial Microbiology; D020071:Interspersed Repetitive Sequences; D053858:Metabolic Networks and Pathways; D008670:Metals / Q000633:toxicity; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004269:DNA, Bacterial; D008670:Metals
keywords: Acidithiobacillus thiooxidans; Adaptation; Bioleaching; Comparative genomics