title: Inside the Pan-genome - Methods and Software Overview.
abstract: The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be "open" as long as new genes are added significantly to the total repertoire for each new additional genome and "closed" when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.
authors.affiliation: Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil;; Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil;
authors.forename: Luis Carlos
authors.initials: LC
authors.lastname: Guimarães
authors.affiliation: Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil;
authors.forename: Jolanta
authors.initials: J
authors.lastname: Florczak-Wyspianska
authors.affiliation: Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil;
authors.forename: Leandro Benevides
authors.initials: LB
authors.lastname: de Jesus
authors.affiliation: Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil;
authors.forename: Marcus Vinícius Canário
authors.initials: MV
authors.lastname: Viana
authors.affiliation: Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil;
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil;
authors.forename: Rommel Thiago Jucá
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
authors.forename: Siomar de Castro
authors.initials: Sde C
authors.lastname: Soares
authors.affiliation: Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
authors.forename: Siomar de Castro
authors.initials: Sde C
authors.lastname: Soares
keywords: Accessory genome; Comparative genome; Core genome; Pan-genome; Species-specific genome