To have a representative set of the
liver contigs of B. microlepidotus, reads of each individual were mapped back to the assembled transcriptome using the alignment program TMAP (http://github.com/iontorrent/TMAP/tarball/tmap.0.3.7) (for more details see Supplementary methods) and contigs showing expression in the three individuals were chosen. In total 13,724 contigs (Supplementary information 1) with an average length of 836.8 bp were retained for the functional annotation ( Table 1; Fig. 1A). The raw sequence data is accessioned in the NCBI Sequence Read Archive (SRA accession SRP046041). The Blastx function was performed with a minimum E-value score of 1.0E− 06 and the gene ontology (GO) terms of molecular function, cellular component, and biological process were GKT137831 price assigned to the 13,724 retained contigs using the Blast2GO software (Conesa et al., 2005). A total of 2803 sequences presented Blast results and 7938 (57.8%) sequences were successfully annotated (Fig. S1, Supplementary information 2). As expected, the species distribution of the Blast hits showed that most hits correspond to fish species (Fig. S2, Supplementary information 2). A total of 40,814 annotations (Supplementary information 3) for the 13,724 contigs were obtained; the biological processes class was the most highly represented (44.2%), followed
by molecular function (35%) and cellular component (20.8%) (Fig. 1B). These proportions were similar to these described for Oncorchynchus mykiss ( Fox et al.,
2014). For B. microlepidotus, the biological see more processes involved mainly the diversity of gene expression, with Mannose-binding protein-associated serine protease predominance of cellular, metabolic and single-organism processes ( Fig. 2A), while the GO annotations for molecular functions were mostly represented by binding and catalytic activity ( Fig. 2B). The cellular component class was mainly composed of cell, organelle, membrane and macromolecular complex components ( Fig. 2C). See Supplementary methods for details regarding functional annotation. The following are the supplementary data related to this article. Supplementary methods We thank C Quezada-Romegialli, JP Oyanedel and P Muñoz-Rojas for support during field work and Dr. Arne Nolte for support during the analyses. The authors thank R Espejo and Omics-Solutions Chile for sequencing. DV thanks Basal Grant PFB 023, ICM P05-002 and Nucleo Milenio NC120030; CVR thanks Conicyt Doctoral Fellowship 21090188 and doctoral thesis fellowship 24121005. All analyses were conducted in Chile and complied with its existing laws (Resolución Exenta No. 3329 Subsecretaria de Pesca). “
“Brine shrimp (Artemia franciscana) are small crustaceans found worldwide, mainly in hypersaline environments. This zooplanktonic organism has been extensively used in fish aquaculture as larval feed for over 85% of cultured species ( Kayim et al., 2010). Besides this role in aquaculture, Artemias spp.