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

Author(s)

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

Affiliation

^[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

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 11, n. 1 FEB 15 2021.
• Web of Science Citations: 0

Abstract

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)

• FAPESP's process: 16/20258-0 - Visceral leishmaniasis: genomics approaches for integrated molecular analysis of host and parasite
• Grantee: Sandra Regina Costa Maruyama
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 17/16328-6 - Visceral Leishmaniasis: genomics approaches for integrated molecular analysis of host and parasite.
• Grantee: Sandra Regina Costa Maruyama
• Support Opportunities: Scholarships in Brazil - Young Researchers
• FAPESP's process: 18/26799-9 - Phenotypic characterization and genomic analysis of Crithidia-like parasites obtained from patients diagnosed with visceral leishmaniasis
• Grantee: Luana Aparecida Rogerio
• Support Opportunities: Scholarships in Brazil - Master