The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

BMC Genomics

Research Article

Toni Gabaldón¹  Larissa L. S. Scholte²  Guilherme Oliveira³  Daniella C. Bartholomeu⁴  Hugo O. Valdivia⁵ 

[1] Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain;Universitat Pompeu Fabra (UPF), Barcelona, Spain;Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain;Genomics and Computational Biology Group, Centro de Pesquisas René Rachou, Belo Horizonte, Brazil;Genomics and Computational Biology Group, Centro de Pesquisas René Rachou, Belo Horizonte, Brazil;Instituto Tecnológico Vale – ITV, Belém, Brazil;Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antonio Carlos, 6627 – Pampulha, 31270-901, Belo Horizonte, MG, Brazil;Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru;Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antonio Carlos, 6627 – Pampulha, 31270-901, Belo Horizonte, MG, Brazil;Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru;Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru;

关键词: Phylogenomics;    Leishmania;    Homology prediction;   

DOI  :  10.1186/s12864-015-2091-2

 received in 2015-05-22, accepted in 2015-10-15,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundLeishmaniasis 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.ResultsThe 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.ConclusionsOur 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).

【 授权许可】

CC BY   
© Valdivia et al. 2015