Growth differentiation factor 9 and bone morphogenetic protein 15 expression in previtellogenic oocytes and during early embryonic development of Yellow-tail Kingfish Seriola lalandi

© 2014 Palomino et al. Background: During fish oocyte maturation, specific molecules are expressed and accumulated within oocyte until fertilization and embryo development. Special attention have been paid in members of the transforming growth factor (TGF-β) superfamily; growth differentiation factor 9 (GDF9/gdf9) and bone morphogenetic protein 15 (BMP15/bmp15), which exert regulatory functions during oocyte maturation and follicle development. However, little attention has been paid to the involvement of these molecules during embryogenesis considering its importance for the formation of a good quality egg and subsequent embryo survival. The purpose of this study was to analyze the expression of gdf9 and bmp15 in previtellogenic oocytes and during early embryonic development in Seriola lalandi, a pelagic fish with increasing prospect for its aquaculture development, which however, show high mortality at embryo and larval stages. Results: Through RT-qPCR it was found that gdf9 express

Data from: A comprehensive transcriptome of early development in yellowtail kingfish (Seriola lalandi)

Seriola lalandi is an ecologically and economically important species that is globally distributed in temperate and subtropical marine waters. The aim of this study was to identify large numbers of genic single nucleotide polymorphisms (SNPs) and differential gene expression (DGE) related to the early development of normal and deformed S. lalandi larvae using high-throughput RNA-Seq data. A de novo assembly of reads generated 40,066 genes ranging from 300 bases to 64,799 bases with an N90 of 788 bases. Homology search and protein signature recognition assigned gene ontology (GO) terms to a total of 15,744 (39.34%) genes. A search against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) retrieved 6,808 KEGG Orthology (KO) identifiers for 10,520 genes (26.25%), and mapping of KO identifiers generated 337 KEGG pathways. Comparisons of annotated genes revealed that 1,262 genes were down-regulated and 1,047 genes were up-regulated in the deformed larvae group compared to the normal group of larvae. Additionally, we identified 6,989 high quality SNPs from the assembled transcriptome. These putative SNPs contain 4,415 transitions and 2,574 transversions, which will be useful for further ecological studies of S. lalandi. This is the first study to use a global transcriptomic approach in S. lalandi, and the resources generated can be used further for investigation of gene expression of marine teleosts to investigate larval developmental biology. The results of the GO enrichment analysis highlight the crucial role of the extracellular matrix in normal skeleton development, which could be important for future studies of skeletal deformities in S. lalandi and other marine species

BLAST results, Annotation information, Gene Ontology (.dat file for Blast2GO)

Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database, InterProScan search result for functional signature of protein domain. Gene Ontology information based on best hit gene matches and KEGG result

Transcriptomic analysis of spleen infected with infectious salmon anemia virus reveals distinct pattern of viral replication on resistant and susceptible Atlantic salmon (Salmo salar)

The infectious salmon anemia virus (ISAv) produces a systemic infection in salmonids, causing large losses in salmon production. However, little is known regarding the mechanisms exerting disease resistance. In this paper, we perform an RNA-seq analysis in Atlantic salmon challenged with ISAv (using individuals coming from families that were highly susceptible or highly resistant to ISAv infection). We evaluated the differential expression of both host and ISAv genes in a target organ for the virus, i.e. the spleen. The results showed differential expression of host genes related to response to stress, immune response and protein folding (genes such as; atf3, mhc, mx1-3, cd276, cd2, cocs1, c7, il10, il10rb, il13ra2, ubl-1, ifng, ifngr1, hivep2, sigle14 and sigle5). An increased protein processing activity was found in susceptible fish, which generates a subsequent unfolded protein response. We observed extreme differences in the expression of viral segments between susceptible and resistant groups, demonstrating the capacity of resistant fish to overcome the virus replication, generating a very low viral load. This phenomenon and survival of this higher resistant fish seem to be related to differences in immune and translational process, as well as to the increase of HIV-EP2 (hivep2) transcript in resistant fish, although the causal mechanism is yet to be discovered. This study provides valuable information about disease resistance mechanisms in Atlantic salmon from a host-pathogen interaction point of view

Pathways-K_numbers_contigs-ID

This is a text file containing all the pathways reconstructed in KEGG automatic annotation server from this RNA-seq study. All the pathways and the K-numbers (each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy) along with contigs-id associated with corresponding K-number are presented in one file. One can search specific pathways of interest and can note the K numbers and contigs-id therein. There after, these contigs-id can be interrogated in blast2go.dat file to obtain fasta sequences of gene/set of genes from the pathway of interest (in order to design primers or other purpose)

BLAST results, Annotation information, Gene Ontology (.dat file for Blast2GO)

Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database, InterProScan search result for functional signature of protein domain. Gene Ontology information based on best hit gene matches and KEGG result

Table containing differential expressed genes (result of edgeR)

This table contains data of list of genes that were < 0.01 FDR value and differed in their expression value at least 2 fold between two group

Information on SNPs identified from transcriptome data (vcf file)

The details of SNPs calling are described in Materials and method

The mapping count table

This count table was used as an input for differential gene expression analysis in edge

Sequences of S. lalandi transcriptome (fasta file)

Transcriptome contigs assembled from filtered paired end sequencing reads on Illumina HiSeq™ 2000 platform using Trinity. Only non-redundant (cluster in CAP3), more than 300bp contigs with open reading frame were kep