CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.

TitleCALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.
Publication TypeJournal Article
Year of Publication2023
AuthorsHongo JAugusto, de Castro GMarques, Menezes APelri Albu, Picorelli AC├ęsar Rio, da Silva TTayroni Ma, Imada ELuidy, Marchionni L, Del-Bem L-E, Chaves AVieira, Almeida GMagno de F, Campelo F, Lobo FPereira
JournalPatterns (N Y)
Volume4
Issue6
Pagination100728
Date Published2023 Jun 09
ISSN2666-3899
Abstract

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.

DOI10.1016/j.patter.2023.100728
Alternate JournalPatterns (N Y)
PubMed ID37409050
PubMed Central IDPMC10318336
Related Faculty: 
Eddie Luidy Imada, Ph.D. Luigi Marchionni, M.D., Ph.D.

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