title: The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships.
abstract: BACKGROUND
  Leishmaniasis is a neglected parasitic disease with diverse clinical manifestations and a complex epidemiology. It has been shown that its parasite-related traits vary between species and that they modulate infectivity, pathogenicity, and virulence. However, understanding of the species-specific adaptations responsible for these features and their evolutionary background is limited. To improve our knowledge regarding the parasite biology and adaptation mechanisms of different Leishmania species, we conducted a proteome-wide phylogenomic analysis to gain insights into Leishmania evolution.
  
  
  RESULTS
  The analysis of the reconstructed phylomes (totaling 45,918 phylogenies) allowed us to detect genes that are shared in pathogenic Leishmania species, such as calpain-like cysteine peptidases and 3'a2rel-related proteins, or genes that could be associated with visceral or cutaneous development. This analysis also established the phylogenetic relationship of several hypothetical proteins whose roles remain to be characterized. Our findings demonstrated that gene duplication constitutes an important evolutionary force in Leishmania, acting on protein families that mediate host-parasite interactions, such as amastins, GP63 metallopeptidases, cathepsin L-like proteases, and our methods permitted a deeper analysis of their phylogenetic relationships.
  
  
  CONCLUSIONS
  Our results highlight the importance of proteome wide phylogenetic analyses to detect adaptation and evolutionary processes in different organisms and underscore the need to characterize the role of expanded and species-specific proteins in the context of Leishmania evolution by providing a framework for the phylogenetic relationships of Leishmania proteins. Phylogenomic data are publicly available for use through PhylomeDB (http://www.phylomedb.org).
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antonio Carlos, 6627 - Pampulha, Belo Horizonte, MG, 31270-901, Brazil. hvalrod@hotmail.com.|Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru. hvalrod@hotmail.com.|Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru. hvalrod@hotmail.com.
authors.forename: Hugo O
authors.initials: HO
authors.lastname: Valdivia
authors.affiliation: Genomics and Computational Biology Group, Centro de Pesquisas René Rachou, Belo Horizonte, Brazil. larissa@cpqrr.fiocruz.br.
authors.forename: Larissa L S
authors.initials: LL
authors.lastname: Scholte
authors.affiliation: Genomics and Computational Biology Group, Centro de Pesquisas René Rachou, Belo Horizonte, Brazil. oliveira@cpqrr.fiocruz.br.|Instituto Tecnológico Vale - ITV, Belém, Brazil. oliveira@cpqrr.fiocruz.br.
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain. toni.gabaldon@crg.eu.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. toni.gabaldon@crg.eu.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. toni.gabaldon@crg.eu.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antonio Carlos, 6627 - Pampulha, Belo Horizonte, MG, 31270-901, Brazil. daniella@icb.ufmg.br.|Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru. daniella@icb.ufmg.br.
authors.forename: Daniella C
authors.initials: DC
authors.lastname: Bartholomeu
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D023281:Genomics; D006657:Histones / Q000235:genetics; D007891:Leishmania / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D020543:Proteome; D015800:Protozoan Proteins / Q000235:genetics*
chemical_list: D006657:Histones; D020543:Proteome; D015800:Protozoan Proteins