Transcriptome of Atlantic Cod (Gadus morhua L.) Early Embryos from Farmed and Wild Broodstocks

Abstract

A number of efforts have been made to elucidate factors regulating egg quality in fish. Recently, we have shown that eggs originating from wild broodstock (WB) of Atlantic cod (Gadus morhua) are of superior quality to those derived from farmed broodstock (FB), and this is associated with differences in chemical composition of egg yolk. However, non-yolk cytoplasmic components accumulated during oogenesis, such as maternal transcripts, have not been studied extensively in fish. The aim of the present study was to characterize putative maternal mRNA transcriptome in fertilized eggs of Atlantic cod, and to compare transcript pools between WB and FB in order to investigate the relation between egg developmental potential and putative maternal mRNA deposits. We performed high-throughput 454 pyrosequencing. For each WB and FB groups, five cDNA libraries were individually tagged and sequenced, resulting in 98,687 (WB) and 119,333 (FB) average reads per library. Sequencing reads were de novo assembled, annotated, and mapped. Out of 13,726 identified isotigs, 238 were differentially expressed between WB and FB, with 155 isotigs significantly upregulated (P<0.05; fold change ≥2.0) in WB. The sequence reads were mapped to 11,340 different Atlantic cod transcripts and 158 sequences were differentially expressed between the two groups. Important transcripts involved in fructose metabolism, fatty acid metabolism, glycerophospholipid metabolism and oxidative phosphorylation were differentially represented between the two broodstock groups, showing potential as biomarkers of egg quality in teleosts. Our findings contribute to the hypothesis that maternal mRNAs affect the egg quality and, consequently, early development of fish.

Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus

“…Perhaps not surprisingly, the protein-coding transcriptome of 1–2 cell stage embryos from A. limnaeus shares many similarities with fertilized eggs from other teleosts when analyzed on a presence–absence basis [17, 43, 44, 48, 49] and GO analysis indicates similar function between the transcriptomes of A. limnaeus and D. rerio . Early vertebrate development is thought to be highly constrained and conserved, and thus, it is reasonable to hypothesize that similar gene expression patterns would be required in all species.…”

“…A great deal of work has gone into characterizing these shared molecular pathways, while relatively few studies have focused on gene expression changes that may underlie plasticity during vertebrate development [40]. In fact, the vast majority of gene expression studies on developing vertebrates have focused on systems that exhibit little to no intraspecific plasticity in development [41–43]. Here, we report on the transcriptome of newly fertilized eggs of the annual killifish A. limnaeus collected from females that are known to produce 100% escape and 100% diapausing embryos.…”

Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)

“…6), and it has been shown that they play an important role in several biological process including development. The developmental profiles of miRNAs have been reported in zebrafish (64), fugu Tetraodon (6), medaka (52), Asian seabass (92), Atlantic cod (46), Japanese flounder (23), and Atlantic halibut (7). The identification of novel miRNAs, thus not yet described in any other species, has not been aimed in the present work, instead miRNAs characterized in other species but not yet described in the European seabass were detected.…”

“…71), nutrition (27), salinity tolerance (9), as well as late larval development and metamorphosis (16). Several high-throughput transcriptomic studies have also be performed in other species of commercial interest, like, e.g., the gilt-head sea bream (Sparus aurata), Atlantic cod (Gadus morhua), and catfish (Ictalurus punctatus) (10,46,55). However, little or no attention has been paid to paralogous genes despite the FSGD event that also gave rise to changes in regulatory control (22,40,80,84).…”

Endocrinology: Advances through omics and related technologies

“…Egg quality has also been suggested to be linked to maternal inheritance of transcripts (Aegerter et al, 2005;Mommens et al, 2010). For instance, Lanes et al (2013)performed a large-scale analysis of the transcriptome at early embryonic stage in Atlantic cod comparing fertilized eggs from wild and farmed animals finding significant differences in fructose metabolism, fatty acid metabolism, glycerophospholipid metabolism, and oxidative phosphorylation. Gracey et al (2004) used an integrative, multi-tissue analysis of the transcriptome of a poikilothermic vertebrate, the common carp Cyprinus carpio, identifying a range of candidate genes endowing thermotolerance and revealing a previously unknown scale and complexity of responses at the level of cellular and tissue function (Gracey et al, 2004).…”