Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex

Soares et al. BMC Genomics Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex Marco Aurlio Soares 1 4 Roberta Amlia de Carvalho Arajo 1 4 Marjorie Mendes Marini 2 Luciana Mrcia de Oliveira 0 3 6 Leonardo Gomes de Lima 5 Viviane de Souza Alves 1 4 Maria Sueli Soares Felipe 8 Marcelo Macedo Brigido 8 Celia Maria de Almeida Soares 7 Jose Franco da Silveira 2 Jeronimo Conceio Ruiz 6 Patrcia Silva Cisalpino 0 1 3 4 0 Programa de Pos-graduacao em Bioinformatica, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais , 31270-901 Belo Horizonte, MG , Brazil 1 Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais , 31270-901 Belo Horizonte, MG , Brazil 2 Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de Sao Paulo , 04023-062 Sao Paulo, SP , Brazil 3 Programa de Pos-graduacao em Bioinformatica, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais , 31270-901 Belo Horizonte, MG , Brazil 4 Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais , 31270-901 Belo Horizonte, MG , Brazil 5 Departamento de Biologia Geral, Universidade Federal de Minas Gerais , Belo Horizonte, MG , Brazil 6 Grupo Informatica de Biossistemas, Centro de Pesquisas Rene Rachou, FIOCRUZ-Minas , 30190-002 Belo Horizonte, MG , Brazil 7 Laboratorio de Biologia Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Goias , 74001-970 Goiania, GO , Brazil 8 Laboratorio de Biologia Molecular, Instituto de Ciencias Biologicas, Universidade de Brasilia , 70910-900 Brasilia, DF , Brazil Background: 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. In this work, we aimed to identify potentially active retrotransposons in Paracoccidioides genomes. Results: We 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. Conclusion: Five 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. - Background 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 can account for 80% or more of total genomic DNA in plants and comprise 45% and 20% of the genomes of metazoans and fungi, respectively [3,4]. 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. Elements belonging to class I are further divided into five orders based on their mechanistic features, organization and reverse transcriptase phylogeny: LTR retrotransposons, DIRS-like elements, Penelope-like elements, LINEs and SINEs [2,6]. LTR retrotransposons are the most widespread, especially those from the Gypsy and Copia superfamilies. Members of the LTR order usually encode two open reading frames (ORFs), one related to viral structural proteins (gag) and the second, known as pol, to a polyprotein composed of an aspartic protease (AP), a reverse transcriptase (RT), an RNase H (RH) and an integrase (IN) [2,6]. Although fungal genomes generally contain fewer repetitive sequences than higher eukaryotes, TEs are viewed as central agents in the evolution of fungal genomes [2,3,7]. In Magnaporthe oryzae, clusters of TEs were associated with increased rates of chromosomal rearrangements, gene duplication and gene evolution [8]. There is an apparent correlation between TE clustering and chromosomal polymorphism in Fusarium oxysporum [9], and in Aspergillus niger, recombination mediated by retrotransposons has led to inversions of genomic regions [10]. In Verticillium dahliae, an asexual plant pathogen, chromosomal rearrangements were found to be associated with retrotransposons, and the authors suggest that homologous recombination between highly similar copies of transposable elements might help to generate genetic diversity [11]. Paracoccidioides is a thermally dimorphic fungus that infects approximately 10 million people in Latin America, causing paracoccidioidomycosis, the most prevalent systemic fungal disease in this region and the deep mycosis responsible for the most deaths in immunocompetent individuals in Brazil [12,13]. Until 2006, the genus Paracoccidioides was believed to include only one species: Paracoccidioides brasiliensis [14]. It was only through Multilocus Sequence Typing (MLST) analysis that the genetic variability in this genus, formerly believed to be merely intraspecific and due to geographic polymorphism, was revealed. Four cryptic species, S1, PS2 and PS3, were identified from the P. brasiliensis complex [15,16], as well as the new species Paracoccidioides lutzii (originally called Pb01-like) [17,18]. Since 2009, it has been accepted that the Paracoccidioides genus is composed of four distinct phylogenetic lineages (S1,PS2, PS3 and Pb01-like), which vary in their virulence, culture adaptation and the different host immune responses they induce [15,19,20]. Strain Pb18 is a member of Species 1 (S1), which is composed of 38 isolates among the 65 studied and is distributed across Latin America [15]. The Pb03 isolate belongs to phylogenetic species 2 (PS2), which is composed of one Venez (...truncated)