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Background Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species responsible for schistosomiasis in the Americas, Middle East and Africa. Adult female worms (mated to males) release eggs in the hepatic portal vasculature and are the principal cause of morbidity. Comparative separate transcriptomes of female and male adult worms were previously assessed with using microarrays and Serial Analysis of Gene Expression (SAGE), thus limiting the possibility of finding novel genes. Moreover, the egg transcriptome was analyzed only once with limited bacterially cloned cDNA libraries. Methodology/Principal findings To compare the gene expression of S. mansoni eggs, females, and males, we performed RNA-Seq on these three parasite forms using 454/Roche technology and reconstructed the transcriptome using Trinity de novo assembly. The resulting contigs were mapped to the genome and were cross-referenced with predicted Smp genes and H3K4me3 ChIP-Seq public data. For the first time, we obtained separate, unbiased gene expression profiles for S. mansoni eggs and female and male adult worms, identifying enriched biological processes and specific enriched functions for each of the three parasite forms. Transcripts with no match to predicted genes were analyzed for their protein-coding potential and the presence of an encoded conserved protein domain. A set of 232 novel protein-coding genes with putative functions related to reproduction, metabolism, and cell biogenesis was detected, which contributes to the understanding of parasite biology. Conclusions/Significance Large-scale RNA-Seq analysis using de novo assembly associated with genome-wide information for histone marks in the vicinity of gene models constitutes a new approach to transcriptome analysis that has not yet been explored in schistosomes. Importantly, all data have been consolidated into a UCSC Genome Browser search-and download-tool (http://schistosoma.usp.br/). This database provides new ways to explore the schistosome genome and transcriptome and will facilitate molecular research on this important parasite. ; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2010/51687-8]; European Union's Seventh Framework Programme [602080]; FAPESP; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brasil ; This work was supported by a grant from Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP grant number 2010/51687-8) to SVA and in part by a grant from the European Union's Seventh Framework Programme under grant agreement no. 602080. LA, MSA, FB, KCPO, GTA were supported by fellowships from FAPESP. SVA, JCS and RDM received established investigator fellowship awards from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brasil. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as "Lipid transport and metabolism," "Cell cycle control, cell division, chromosome partitioning" and "Cell motility" were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150-5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks. ; Brazilian Agency CAPESCAPES [3385/2013]; CAPESCAPES [3377/2013]; CNPqNational Council for Scientific and Technological Development (CNPq) [304881/2015-5, 305857/2013-4, 473221/2013-6]; FundectFundect [TO141/2016, TO007/2015] ; This work was partially supported by the Brazilian Agency CAPES (grant number 3385/2013). J.S.L.P. and J.M. were supported by CAPES fellowships. J.C.S. was supported in part by a grant from CNPq (grant number 304881/2015-5). N.F.A. was supported by grants Fundect TO141/2016, TO007/2015, CNPq 305857/2013-4, 473221/2013-6, and CAPES 3377/2013. ; Public domain authored by a U.S. government employee