title: Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. soares05ma@gmail.com.
authors.forename: Marco Aurélio
authors.initials: MA
authors.lastname: Soares
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. robertaamalia@gmail.com.
authors.forename: Roberta Amália
authors.initials: RA
authors.lastname: de Carvalho Araújo
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04023-062, São Paulo, SP, Brazil. marjoriemarini@gmail.com.
authors.forename: Marjorie Mendes
authors.initials: MM
authors.lastname: Marini
authors.affiliation: Programa de Pós-graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. lubios@gmail.com.|Grupo Informática de Biossistemas, Centro de Pesquisas René Rachou, FIOCRUZ-Minas, 30190-002, Belo Horizonte, MG, Brazil. lubios@gmail.com.
authors.forename: Luciana Márcia
authors.initials: LM
authors.lastname: de Oliveira
authors.affiliation: Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil. leonardogdlima@gmail.com.
authors.forename: Leonardo Gomes
authors.initials: LG
authors.lastname: de Lima
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. gouveia_va@yahoo.com.
authors.forename: Viviane
authors.initials: V
authors.lastname: de Souza Alves
authors.affiliation: Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, DF, Brazil. msueliunb@gmail.com.
authors.forename: Maria Sueli Soares
authors.initials: MS
authors.lastname: Felipe
authors.affiliation: Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, DF, Brazil. mmbrigido@gmail.com.
authors.forename: Marcelo Macedo
authors.initials: MM
authors.lastname: Brigido
authors.affiliation: Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil. celia@icb.ufg.br.
authors.forename: Celia Maria
authors.initials: CM
authors.lastname: de Almeida Soares
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04023-062, São Paulo, SP, Brazil. jose.franco@unifesp.br.
authors.forename: Jose Franco
authors.initials: JF
authors.lastname: da Silveira
authors.affiliation: Grupo Informática de Biossistemas, Centro de Pesquisas René Rachou, FIOCRUZ-Minas, 30190-002, Belo Horizonte, MG, Brazil. jeronimo@cpqrr.fiocruz.br.
authors.forename: Jeronimo Conceição
authors.initials: JC
authors.lastname: Ruiz
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. pscisalp@icb.ufmg.br.|Programa de Pós-graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil. pscisalp@icb.ufmg.br.
authors.forename: Patrícia Silva
authors.initials: PS
authors.lastname: Cisalpino
mesh_terms: D016000:Cluster Analysis; D020224:Expressed Sequence Tags / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics; D058977:Molecular Sequence Annotation; D010228:Paracoccidioides / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D018626:Retroelements