The identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenomes or metatranscriptomes, very few of these are able to link taxonomic identity to function or are limited by their input types or databases used. Here we present MetaFunc, a workflow which takes RNA sequences as input reads, and from these (1) identifies species present in the microbiome sample and (2) provides gene ontology annotations associated with the species identified. In addition, MetaFunc allows for host gene analysis, mapping the reads to a host genome, and separating these reads, prior to microbiome analyses. Differential abundance analysis for microbe taxonomies, and differential gene expression analysis and gene set enrichment analysis may then be carried out through the pipeline. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper, we showed how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer.

Angiostrongylus cantonensis is the main aetiological agent of eosinophilic meningoencephalitis in humans. Several outbreaks have been documented around the world, cementing its status as an emerging global public health concern. As a result, new strategies for the diagnosis, prophylaxis and treatment of cerebral angiostrongyliasis are urgently needed. In this study, we report on the de novo assembly of the A. cantonensis transcriptome, its full functional annotation and a reconstruction of complete metabolic pathways. All results are available at AngiostrongylusDB (http://angiostrongylus.lad.pucrs.br/admin/welcome). The aim of this study was to identify the active genes and metabolic pathways involved in the mechanisms of infection and survival inside Rattus norvegicus. Among 389 metabolic mapped pathways, the blood coagulation/antithrombin pathways of heparan sulphate/heparin are highlighted. Moreover, we identified genes codified to GP63 (leishmanolysin), CALR (calreticulin), ACE (peptidyl-dipeptidase A), myoglobin and vWD (von Willebrand factor type D domain protein) involved in the infection invasion and survival of the parasite. The large dataset of functional annotations provided and the full-length transcripts identified in this research may facilitate future functional genomics studies and provides a basis for the development of new techniques for the diagnosis, prevention and treatment of cerebral angiostrongyliasis.

Silene ciliata (Caryophyllaceae) is a key species to test evolutionary hypotheses in a global warming context. The recent advances in Next Generation Sequencing technologies can help in providing clues about climate-mediated local adaptation. In the present study, we analysed the full transcriptome of six individuals of S. ciliata from Central Spain, by aligning it with the transcriptome of S. latifolia. We aimed (a) to identify Single Nucleotide Polymorphisms (SNPs) in the transcriptome of the species, (b) to describe the biological function of the polymorphic genes expressed and (c) to identify loci that may be involved in local adaptation processes at optimal and marginal populations of the species. We identified a total of 147,118 SNPs distributed throughout 12,688 sequences. The number of polymorphic sequences annotated was 8023. One hundred thirty sequences containing polymorphisms strongly associated with optimal and marginal conditions were selected. Gene ontology searches were successful for 118, and many of these were related to responses to stress (n = 19) and abiotic stimulus (n = 16). Genomic data generated provide a starting point for further research on the identification of candidate genes related to local adaptation and other processes in the species.

Lasallia hispanica (Frey) Sancho & A. Crespo is one of three Lasallia species occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxon L. pustulata in the supra- and oro-Mediterranean belts. We sequenced the genome of L. hispanica from a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome of L. hispanica to the closely related, yet ecologically distant, L. pustulata and found high synteny in gene content and order. The newly assembled and annotated L. hispanica genome represents a useful resource for future investigations into niche differentiation, speciation and microevolution in L. hispanica and other members of the genus.

An adverse early life environment can increase the risk of metabolic and other disorders later in life. Genetic variation can modify an individual’s susceptibility to these environmental challenges. These gene by environment interactions are important, but difficult, to dissect. The nucleus is the primary organelle where environmental responses impact directly on the genetic variants within the genome, resulting in changes to the biology of the genome and ultimately the phenotype. Understanding genome biology requires the integration of the linear DNA sequence, epigenetic modifications and nuclear proteins that are present within the nucleus. The interactions between these layers of information may be captured in the emergent spatial genome organization. As such genome organization represents a key research area for decoding the role of genetic variation in the Developmental Origins of Health and Disease.

Based on the sequences of Brassica rapa ssp. pekinensis, we carried out a single-nucleotide polymorphism (SNP) study for genes controlling disease resistance (clubroot, turnip mosaic virus and soft rot) and leaf traits in B. rapa leafy genotypes ‘VC40’ and ‘SR5’. In total, 7645 SNP markers were obtained based on the annotation of a B. rapa database for disease resistance. Among these 7645 SNP markers, 141 were related to 125 genes linked to leaf traits. From these 141 SNP markers, 63 were screened and High Resolution Melt (HRM) primers were designed for genomic studies. A total of 20 polymorphic SNP primers were finally obtained. Eventually, these markers will be further used for the detection of quantitative trait loci and mapping studies.