Diversity and genome mapping assessment of disordered and functional domains in trypanosomatids

Avelar, Grace Santos Tavares; Gonçalves, Leilane Oliveira; Guimarães, Frederico Gonçalves; Guimarães, Paul Anderson Souza; Rocha, Luiz Gustavo do Nascimento; Carvalho, Maria G.; Resende, Daniela de Melo; Ruiz, Jerônimo C.

doi:10.1016/j.jprot.2020.103919

Cited by 2 publications

(1 citation statement)

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“…TriTrypDB's and Swiss-Prot's annotations of protein sequences comprising our reference data set revealed pseudogenic and intergenic CDS counterparts of numerous known multigenic families in trypanosomatids ( Avelar et al 2020 ) and several other protein classes. However, most pseudogenes and intergenic CDSs identified remain unclassified as their most similar proteins in the reference group are annotated as hypothetical , unspecified , putative , pseudogene , or pseudogenic —Lm (1,074/95.8%), Tb (2,074/98.1%), and Tc (4,828/91.3%).…”

Section: Resultsmentioning

confidence: 99%

Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes

Costa

Machado

Álvarez-Valín

et al. 2022

Genome Biology and Evolution

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Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion, and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames (ORFs), with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.

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Section: Resultsmentioning

confidence: 99%