Abstract
BackgroundSpecies from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil. We previously described the identification of eight new families of DNA transposons in Paracoccidioides genomes. In this work, we aimed to identify potentially active retrotransposons in Paracoccidioides genomes.ResultsWe identified five different retrotransposon families (four LTR-like and one LINE-like element) in the genomes of three Paracoccidioides isolates. Retrotransposons were present in all of the genomes analyzed. P. brasiliensis and P. lutzii species harbored the same retrotransposon lineages but differed in their copy numbers. In the Pb01, Pb03 and Pb18 genomes, the number of LTR retrotransposons was higher than the number of LINE-like elements, and the LINE-like element RtPc5 was transcribed in Paracoccidioides lutzii (Pb01) but could not be detected in P. brasiliensis (Pb03 and Pb18) by semi-quantitative RT-PCR.ConclusionFive new potentially active retrotransposons have been identified in the genomic assemblies of the Paracoccidioides species complex using a combined computational and experimental approach. The distribution across the two known species, P. brasiliensis and P. lutzii, and phylogenetics analysis indicate that these elements could have been acquired before speciation occurred. The presence of active retrotransposons in the genome may have implications regarding the evolution and genetic diversification of the Paracoccidioides genus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1564-7) contains supplementary material, which is available to authorized users.
Highlights
Species from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil
Clustering, similarity and functional annotation of Paracoccidioides EST sequences As shown in the workflow in Figure 1, the first step in the identification of active retrotransposons in the genomes of the Paracoccidioides species complex was to access the information contained in the EST database
A local database was built with 41,558 downloaded Paracoccidioides ESTs, which were clustered, resulting in 12,922 sequence clusters distributed in 4,812 contigs and 8,110 singlets
Summary
Species from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil. We previously described the identification of eight new families of DNA transposons in Paracoccidioides genomes. Transposable elements (TEs) have been found in virtually all eukaryotic species investigated to date [1,2] and may represent a significant portion of the genomes of living organisms. TEs are DNA sequences with the ability to move from one genomic location to another and can be grouped in two classes according to whether their transposition intermediate is RNA (class I or retrotransposons) or DNA (class II or DNA transposons) [2,5]. Retrotransposons replicate by a “copy and paste” process, whereby the RNA intermediate is reverse-transcribed into double-stranded (ds) DNA by enzymes encoded by the TEs themselves.
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