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First Steps in the Analysis of Prokaryotic Pan-Genomes
Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418249/ https://www.ncbi.nlm.nih.gov/pubmed/32843837 http://dx.doi.org/10.1177/1177932220938064 |
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author | Costa, Sávio Souza Guimarães, Luís Carlos Silva, Artur Soares, Siomar Castro Baraúna, Rafael Azevedo |
author_facet | Costa, Sávio Souza Guimarães, Luís Carlos Silva, Artur Soares, Siomar Castro Baraúna, Rafael Azevedo |
author_sort | Costa, Sávio Souza |
collection | PubMed |
description | Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues. |
format | Online Article Text |
id | pubmed-7418249 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-74182492020-08-24 First Steps in the Analysis of Prokaryotic Pan-Genomes Costa, Sávio Souza Guimarães, Luís Carlos Silva, Artur Soares, Siomar Castro Baraúna, Rafael Azevedo Bioinform Biol Insights Review Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues. SAGE Publications 2020-08-07 /pmc/articles/PMC7418249/ /pubmed/32843837 http://dx.doi.org/10.1177/1177932220938064 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Review Costa, Sávio Souza Guimarães, Luís Carlos Silva, Artur Soares, Siomar Castro Baraúna, Rafael Azevedo First Steps in the Analysis of Prokaryotic Pan-Genomes |
title | First Steps in the Analysis of Prokaryotic Pan-Genomes |
title_full | First Steps in the Analysis of Prokaryotic Pan-Genomes |
title_fullStr | First Steps in the Analysis of Prokaryotic Pan-Genomes |
title_full_unstemmed | First Steps in the Analysis of Prokaryotic Pan-Genomes |
title_short | First Steps in the Analysis of Prokaryotic Pan-Genomes |
title_sort | first steps in the analysis of prokaryotic pan-genomes |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418249/ https://www.ncbi.nlm.nih.gov/pubmed/32843837 http://dx.doi.org/10.1177/1177932220938064 |
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