Developmental biology of intensively reared flatfish

Aquaculture production of Solea solea is based mostly on wild-caught breeders. A consistent good quality and quantity of produced eggs throughout the year, and of next-generation broodstock, is important for reducing the overall cost of production. Hox genes have a crucial role in controlling embryonic development and their genetic variation could alter the phenotype dramatically. Direct association of polymorphism in hoxa1a, hoxa2a & hoxa2b of sole with egg viability indicates hoxa2b as a potential genetic marker. HRM analysis was carried out in 52 viable and 61 non-viable eggs collected at 48 hours post fertilization (hpf). Allelic and genotypic frequencies of polymorphism were analyzed and results illustrated a significantly increased risk for non-viability for minor alleles and their homozygous genotypes. Haplotype analysis demonstrated a significant recessive effect on the risk of non-viability, by increasing the odds of disrupting embryonic development up to three-fold. Phylogenetic analysis showed that the paralog genes hoxa2a and hoxa2b, are separated distinctly in two clades and presented a significant ω variation, revealing their diverged evolutionary rate. Alterations of hox genes temporal expression level may be important. Expression analysis of hoxa1a, hoxa2a, hoxa2b, hoxb1a, hoxb1b and hoxa13a genes was carried out. Results revealed a premature and/or maternal expression of hoxa13a in embryos, and the detection of hoxa2a and hoxa2b genes as members of paralog group 2. PCA of hox gene expression in 48 hpf embryos coming from wild-caught broodstock and a first-generation one reared in the hatchery, unveiled that these broodstocks are clearly distinct. In addition, their pairwise comparison revealed significant differences in the expression levels of hoxb1a and hoxb1b genes. Enzymes involved in Docosahexaenoic acid (DHA) synthesis play also a pivotal role in normal embryonic development. Recently, evidence of an alternative Δ4fad-dependent DHA synthesis pathway, including elovl5 activity, was presented in Solea senegalensis implying the biosynthesis of DHA directly from eicosapentaenoic acid (EPA). In order to investigate if this alternative pathway in Solea solea, expression analysis was carried out for Δ4-fattyacyldesaturase (Δ4fad) and 5elongase (elovl5). Results revealed Δ4fad expression in sole eggs and a significant up-regulation in larvae. Additionally, we introduce a visual framework in the environment of a main computer algebra system (CAS), Mathematica, to picture variations and evolution schemes in gene expression. Our computational approach constructs snapshots for gene expression profiles, with the advantage of being self-evident, concise and clear. Divergence from normal coloring has an impact on the survival of the species in the marine environment as well as on the sales price of farmed animals. Analysis of whole transcriptome between normally pigmented and ambicolorated juveniles was performed by using NGS techniques. Results revealed that ambicolorated juveniles exhibit a divergent function mainly of the central nervous system at the synaptic level, as well as the ionic channels that affect also the muscular and cardiac function.Στην υδατοκαλλιέργεια, η εκτροφή του είδους Solea solea βασίζεται κυρίως στην αλίευση και στην ελεγχόμενη αναπαραγωγή εγκλιματισμένων άγριων γεννητόρων. Η ποιότητα και η ποσότητα των παραγόμενων ωών καθ’ όλη τη διάρκεια του έτους είναι σημαντικές για τη μείωση του συνολικού κόστους εκτροφής του είδους. Τα ομοιοτικά γονίδια συνδράμουν καθοριστικά στον έλεγχο της εμβρυϊκής ανάπτυξης. Η συσχέτιση του πολυμορφισμού των ομοιοτικών γονιδίων hoxa1a, hoxa2a & hoxa2b με τη βιωσιμότητα των ωών της γλώσσας υποδεικνύει το hoxa2b ως πιθανό γενετικό δείκτη. Ανάλυση HRM διεξήχθη σε 52 βιώσιμα και 61 μη βιώσιμα αυγά που συλλέχθηκαν 48 ώρες μετά τη γονιμοποίηση (hpf). Οι αλληλομορφικές και γονοτυπικές συχνότητες του πολυμορφισμού αναλύθηκαν και τα αποτελέσματα υποδεικνύουν σημαντικά αυξημένο κίνδυνο μη βιωσιμότητας για τα ελάσσονα αλληλόμορφα και τους ομόζυγους γονότυπούς τους. Η ανάλυση απλοτύπων κατέδειξε σημαντική επίδραση αυξάνοντας τις πιθανότητες διακοπής της εμβρυϊκής ανάπτυξης έως και τρεις φορές. Η φυλογενετική ανάλυση των παράλογων γονιδίων hoxa2a και hoxa2b, έδειξε πως διαχωρίζονται σε δύο διακριτούς κλάδους και παρουσιάζουν σημαντική διακύμανση της τιμής ω, που δηλώνει αποκλίνοντες ρυθμούς εξέλιξης. Οι μεταβολές στο χρόνο έκφρασης των ομοιοτικών γονιδίων μπορεί να είναι καθοριστικές. Εν προκειμένω, διεξήχθη ανάλυση έκφρασης των γονιδίων hoxa1a, hoxa2a, hoxa2b, hoxb1a, hoxb1b και hoxa13a. Τα αποτελέσματα αποκάλυψαν μια πρόωρη και / ή μητρικής προέλευσης έκφραση του hoxa13a και την ανίχνευση των γονιδίων hoxa2a και hoxa2b ως μέλη της παραλογικής ομάδας 2. Η Ανάλυση Κυρίων Συνιστωσών της γονιδιακής έκφρασης των ομοιοτικών γονιδίων σε έμβρυα 48 hpf που προέρχονται από άγριους γεννήτορες και από γεννήτορες πρώτης γενιάς, αποκάλυψε ότι οι δύο ομάδες διαχωρίζονται καθαρά. Επιπλέον, η σύγκρισή κατά ζεύγη αποκάλυψε σημαντικές διαφορές στα επίπεδα έκφρασης των γονιδίων hoxb1a και hoxb1b. Ο ρόλος του εικοσιδυαεξαενοϊκού οξέος (DHA) είναι εξίσου σημαντικός στην φυσιολογική εμβρυϊκή ανάπτυξη. Πρόσφατα, περιγράφηκε στο είδος Solea senegalensis, ένα εναλλακτικό μονοπάτι σύνθεσης DHA που εξαρτάται από τη δράση των Δ4fad και elovl5, και υποδηλώνει τη βιοσύνθεση του DHA απευθείας από το εικοσαπενταενοϊκό οξύ (EPA). Προκειμένου να διερευνηθεί εάν αυτή η εναλλακτική οδός απαντάται στο είδος Solea solea διεξήχθη ανάλυση έκφρασης για τα γονίδια Δ4fad και elovl5. Τα αποτελέσματα αποκάλυψαν την έκφραση του γονιδίου Δ4fad στα ωά γλώσσας και σημαντική του αυξορρύθμιση στις προνύμφες. Αναφορικά με την οπτικοποίηση δεδομένων γονιδιακής έκφρασης (qRT-PCR), δημιουργήθηκε ένα υπολογιστικό πλαίσιο στη διεπιφάνεια ενός συστήματος υπολογιστικής άλγεβρας (CAS λογισμικού). Η υπολογιστική προσέγγιση δημιουργεί στιγμιότυπα γονιδιακής έκφρασης, σε παραλλαγές εικόνας και σχήματα εξέλιξης με το πλεονέκτημα να είναι αυτονόητα, συνοπτικά και σαφή. Τέλος, η απόκλιση από το φυσιολογικό χρωματισμό έχει επίπτωση στην επιβίωση στο περιβάλλον, καθώς και στην τιμή πώλησης των εκτρεφόμενων ατόμων. Η εξέταση του μεταγραφώματος σε επίπεδο γονιδίων και βιολογικών διαδρομών μεταξύ φυσιολογικών και μη φυσιολογικών ατόμων που παρουσιάζουν αμφιχρωματισμό έδειξε ότι τα άτομα με αμφιχρωματισμό, εμφανίζουν αποκλίνουσα λειτουργία κυρίως του κεντρικού νευρικού συστήματος σε επίπεδο συνάψεων, καθώς και των ιοντικών διαύλων που επηρεάζουν επιπλέον τη μυϊκή και καρδιακή λειτουργία

Hox genes polymorphism depicts developmental disruption of common sole eggs

In sole aquaculture production, consistency in the quality of produced eggs throughout the year is unpredictable. Hox genes have a crucial role in controlling embryonic development and their genetic variation could alter the phenotype dramatically. In teleosts genome duplication led paralog hox genes to become diverged. Direct association of polymorphism in hoxa1a, hoxa2a & hoxa2b of Solea solea with egg viability indicates hoxa2b as a potential genetic marker. High Resolution Melt (HRM) analysis was carried out in 52 viable and 61 non-viable eggs collected at 54±6 hours post fertilization (hpf). Allelic and genotypic frequencies of polymorphism were analyzed and results illustrated a significantly increased risk for non-viability for minor alleles and their homozygous genotypes. Haplotype analysis demonstrated a significant recessive effect on the risk of non-viability, by increasing the odds of disrupting embryonic development up to three-fold. Phylogenetic analysis showed that the paralog genes hoxa2a and hoxa2b, are separated distinctly in two clades and presented a significant ω variation, revealing their diverged evolutionary rate

Malpigmentation of common sole (Solea solea) during metamorphosis is associated with differential synaptic-related gene expression

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)– plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones

Hox genes polymorphism depicts developmental disruption of common sole eggs

In sole aquaculture production, consistency in the quality of produced eggs throughout the year is unpredictable. Hox genes have a crucial role in controlling embryonic development and their genetic variation could alter the phenotype dramatically. In teleosts genome duplication led paralog hox genes to become diverged. Direct association of polymorphism in hoxa1a, hoxa2a & hoxa2b of Solea solea with egg viability indicates hoxa2b as a potential genetic marker. High Resolution Melt (HRM) analysis was carried out in 52 viable and 61 non-viable eggs collected at 54±6 hours post fertilization (hpf). Allelic and genotypic frequencies of polymorphism were analyzed and results illustrated a significantly increased risk for non-viability for minor alleles and their homozygous genotypes. Haplotype analysis demonstrated a significant recessive effect on the risk of non-viability, by increasing the odds of disrupting embryonic development up to three-fold. Phylogenetic analysis showed that the paralog genes hoxa2a and hoxa2b, are separated distinctly in two clades and presented a significant ω variation, revealing their diverged evolutionary rate.</p

Hox gene expression profiles during embryonic development of common sole

Common sole (Solea solea) aquaculture production is based mostly on wild-caught breeders. Recently, the successful reproduction of first-generation fish that were reared in captivity was accomplished. A consistent good quality and quantity of produced eggs throughout the year, and of next-generationbroodstock, is important for reducing the overall cost of production. Hox genes play a pivotal role in normal embryonic development and alterations of their temporal expression level may be important for egg viability. Expression profile analysis of five hox genes (hoxa1a, hoxa2a, hoxa2b, hoxb1a and hoxb1b) involved in early embryonic development and of hoxa13a, which is involved in late stages, was carried out. Results revealed a premature and/or maternal expression of hoxa13a in sole embryos,and the detection of hoxa2a and hoxa2b genes as members of paralog group 2. Principal Component Analysis of hox gene expression in 54 ± 6 hours post fertilization embryos coming from wild-caught broodstock and a first-generation one reared in the hatchery, unveiled that these broodstocks are clearly distinct. In addition, their pairwise comparison revealed significant differences in the expression levels of hoxb1a and hoxb1b genes. Hox gene regulation during embryonic development could give valuable insight into rearing sole broodstocks with different origin in concert, and also into gaining a steady mass production of eggs, either in quality or quantity, all year round

Hox gene expression profiles during embryonic development of common sole: Supplementary material

Common sole (<i>Solea solea</i>) aquaculture production is based mostly on wild-caught breeders. Recently, the successful reproduction of first-generation fish that were reared in captivity was accomplished. A consistent good quality and quantity of produced eggs throughout the year, and of next-generation broodstock, is important for reducing the overall cost of production. <i>Hox</i> genes play a pivotal role in normal embryonic development and alterations of their temporal expression level may be important for egg viability. Expression profile analysis of six <i>hox </i>genes (<i>hoxa1a, hoxa2a, hoxa2b, hoxb1a </i>and <i>hoxb1b) </i>involved in early embryonic development and of <i>hoxa13a</i>, which is<i> </i>involved in late stages, was carried out. <a>Results revealed a premature and/or maternal expression of <i>hoxa13a </i>in sole embryos, and the detection of <i>hoxa2a </i>and <i>hoxa2b </i>genes as members of paralog group 2. Principal Component Analysis of <i>hox </i>gene expression in 54 ± 6 hours post fertilization embryos coming from wild-caught broodstock and a first-generation one reared in the hatchery, unveiled that these broodstocks are clearly distinct. In addition, their pairwise comparison revealed significant differences in the expression levels of <i>hoxb1a </i>and <i>hoxb1b</i> genes. </a>Hox gene regulation during embryonic development could give valuable insight into rearing sole broodstocks with different origin in concert, and also into gaining a steady mass production of eggs, either in quality or quantity, all year round