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CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.
Hongo, Jorge Augusto; de Castro, Giovanni Marques; Albuquerque Menezes, Alison Pelri; Rios Picorelli, Agnello César; Martins da Silva, Thieres Tayroni; Imada, Eddie Luidy; Marchionni, Luigi; Del-Bem, Luiz-Eduardo; Vieira Chaves, Anderson; Almeida, Gabriel Magno de Freitas; Campelo, Felipe; Lobo, Francisco Pereira.
Afiliação
  • Hongo JA; Instituto de Computação, Universidade Estadual de Campinas, Campinas, Sao Paulo 13083-872, Brazil.
  • de Castro GM; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Albuquerque Menezes AP; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Rios Picorelli AC; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Martins da Silva TT; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Imada EL; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
  • Marchionni L; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
  • Del-Bem LE; Department of Botany, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Vieira Chaves A; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
  • Almeida GMF; Faculty of Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT The Arctic University of Norway, 9019 Tromsø, Norway.
  • Campelo F; Department of Computer Science, College of Engineering and Physical Sciences, Aston University, Birmingham B4 7ET, UK.
  • Lobo FP; Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
Patterns (N Y) ; 4(6): 100728, 2023 Jun 09.
Article em En | MEDLINE | ID: mdl-37409050
Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli, its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Patterns (N Y) Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Patterns (N Y) Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos