Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes

Autor(es)

Maruyama, Sandra Regina ^[1] ; Rogerio, Luana Aparecida ^[1] ; Freitas, Patricia Domingues ^[1] ; Geraldes Teixeira, Marta Maria ^[2] ; Chaves Ribeiro, Jose Marcos ^[3]

Afiliação do(s) autor(es)

^[1] Fed Univ Sao Carlos UFSCar, Ctr Biol Sci & Hlth, Dept Genet & Evolut, BR-13565905 Sao Carlos, SP - Brazil

^[2] Univ Sao Paulo, ICB, Dept Parasitol, Sao Paulo, SP - Brazil

^[3] NIAID, Vector Biol Sect, Lab Malaria & Vector Res, NIH, 12735 Twinbrook Pkwy Rm 2E32, Rockville, MD 20852 - USA

• Tipo de documento: Artigo Científico
• Fonte: SCIENTIFIC REPORTS; v. 11, n. 1 FEB 15 2021.
• Citações Web of Science: 0

Resumo

The increasing number of available genomic data allowed the development of phylogenomic analytical tools. Current methods compile information from single gene phylogenies, whether based on topologies or multiple sequence alignments. Generally, phylogenomic analyses elect gene families or genomic regions to construct phylogenomic trees. Here, we presented an alternative approach for Phylogenomics, named TOMM (Total Ortholog Median Matrix), to construct a representative phylogram composed by amino acid distance measures of all pairwise ortholog protein sequence pairs from desired species inside a group of organisms. The procedure is divided two main steps, (1) ortholog detection and (2) creation of a matrix with the median amino acid distance measures of all pairwise orthologous sequences. We tested this approach within three different group of organisms: Kinetoplastida protozoa, hematophagous Diptera vectors and Primates. Our approach was robust and efficacious to reconstruct the phylogenetic relationships for the three groups. Moreover, novel branch topologies could be achieved, providing insights about some phylogenetic relationships between some taxa. (AU)

• Processo FAPESP: 16/20258-0 - Leishmaniose visceral: abordagens genômicas para análise molecular integrada do hospedeiro e do parasito
• Beneficiário: Sandra Regina Costa Maruyama
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 17/16328-6 - Leishmaniose Visceral: abordagens genômicas para análise molecular integrada do hospedeiro e do parasito.
• Beneficiário: Sandra Regina Costa Maruyama
• Modalidade de apoio: Bolsas no Brasil - Jovens Pesquisadores
• Processo FAPESP: 18/26799-9 - Caracterização fenotípica e análise genômica de parasitos Crithidia-like obtidos de pacientes diagnosticados com leishmaniose visceral
• Beneficiário: Luana Aparecida Rogerio
• Modalidade de apoio: Bolsas no Brasil - Mestrado