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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Gene Tags Assessment by Comparative Genomics (GTACG ): A User-Friendly Framework for Bacterial Comparative Genomics

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Author(s):
do Nascimento Santiago, Caio Rafael [1, 2] ; Barbosa Assis, Renata de Almeida [3] ; Moreira, Leandro Marcio [3, 4] ; Digiampietri, Luciano Antonio [5, 2]
Total Authors: 4
Affiliation:
[1] Univ Sao Paulo, Sao Paulo - Brazil
[2] Univ Sao Paulo, Bioinformat Grad Program, Sao Paulo - Brazil
[3] Univ Fed Ouro Preto, Nucl Pesquisas Ciencias Biol, Biotecnol Grad Program, Ouro Preto - Brazil
[4] Univ Fed Ouro Preto, Dept Biol Sci, Ouro Preto - Brazil
[5] Univ Sao Paulo, Sch Arts Sci & Humanities, Sao Paulo - Brazil
Total Affiliations: 5
Document type: Journal article
Source: FRONTIERS IN GENETICS; v. 10, AUG 26 2019.
Web of Science Citations: 0
Abstract

Genomics research has produced an exponential amount of data. However, the genetic knowledge pertaining to certain phenotypic characteristics is lacking. Also, a considerable part of these genomes have coding sequences (CDSs) with unknown functions, posing additional challenges to researchers. Phylogenetically close microorganisms share much of their CDSs, and certain phenotypes unique to a set of microorganisms may be the result of the genes found exclusively in those microorganisms. This study presents the GTACG framework, an easy-to-use tool for identifying in the subgroups of bacterial genomes whose microorganisms have common phenotypic characteristics, to find data that differentiates them from other associated genomes in a simple and fast way. The GTACG analysis is based on the formation of homologous CDS clusters from local alignments. The front-end is easy to use, and the installation packages have been developed to enable users lacking knowledge of programming languages or bioinformatics analyze high-throughput data using the tool. The validation of the GTACG framework has been carried out based on a case report involving a set of 161 genomes from the Xanthomonadaceae family, in which 19 families of orthologous proteins were found in 90% of the plant-associated genomes, allowing the identification of the proteins potentially associated with adaptation and virulence in plant tissue. The results show the potential use of GTACG in the search for new targets for molecular studies, and GTACG can be used as a research tool by biologists who lack advanced knowledge in the use of computational tools for bacterial comparative genomics. (AU)

FAPESP's process: 18/03428-5 - Dimensions US-BIOTA-Sao Paulo: traits as predictors of adaptive diversification along the Brazilian Dry Diagonal
Grantee:Vera Nisaka Solferini
Support type: BIOTA-FAPESP Program - Thematic Grants