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.
Keywords: Pan-genome, Core genome, Accessory genome, Species-specific genome, Comparative genome.
Current Genomics
Title:Inside the Pan-genome - Methods and Software Overview
Volume: 16 Issue: 4
Author(s): Luis Carlos Guimaraes, Leandro Benevides de Jesus, Marcus Vinicius Canario Viana, Artur Silva, Rommel Thiago Juca Ramos, Siomar de Castro Soares and Vasco Azevedo
Affiliation:
Keywords: Pan-genome, Core genome, Accessory genome, Species-specific genome, Comparative genome.
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.
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Cite this article as:
Carlos Guimaraes Luis, Benevides de Jesus Leandro, Vinicius Canario Viana Marcus, Silva Artur, Thiago Juca Ramos Rommel, de Castro Soares Siomar and Azevedo Vasco, Inside the Pan-genome - Methods and Software Overview, Current Genomics 2015; 16 (4) . https://dx.doi.org/10.2174/1389202916666150423002311
DOI https://dx.doi.org/10.2174/1389202916666150423002311 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
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