Dynamics of gene expression patterns during early development of the European seabass (<i>Dicentrarchus labrax</i>)

Kaitetzidou, Elisavet; Xiang, Jenny; Antonopoulou, Efthimia; Tsigenopoulos, Costas S.; Sarropoulou, Elena

doi:10.1152/physiolgenomics.00001.2015

Cited by 20 publications

(14 citation statements)

References 98 publications

(91 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, GO enrichment analysis of DEGs during the posterior intestine developmental process (4-Dph group, 8-Dph group, 12-Dph group, 20-Dph group, 40- Dph group and Oyd group) of loach was complicated. DEGs obtained here mapped to the enriched GO term cellular process, single-organism process, biological regulation, developmental process and multicellular organismal process, which was also found in European seabass during its early development12. These suggested gene regulation was crucial for achieving various physiological functions associated to the development of loach posterior intestine, which was similar to the intestine regeneration process in sea cucumbers since they endured both proliferation and development13.…”

Section: Discussionmentioning

confidence: 53%

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

Luo

Cao

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Dojo loach, Misgurnus anguillicaudatus is a freshwater fish species of the loach family Cobitidae, using its posterior intestine as an accessory air-breathing organ. Little is known about the molecular regulatory mechanisms in the formation of intestinal air-breathing function of M. anguillicaudatus. Here high-throughput sequencing of mRNAs was performed from six developmental stages of posterior intestine of M. anguillicaudatus: 4-Dph (days post hatch) group, 8-Dph group, 12-Dph group, 20-Dph group, 40-Dph group and Oyd (one-year-old) group. These six libraries were assembled into 81300 unigenes. Totally 40757 unigenes were annotated. Subsequently, 35291 differentially expressed genes (DEGs) were scanned among different developmental stages and clustered into 20 gene expression profiles. Finally, 15 key pathways and 25 key genes were mined, providing potential targets for candidate gene selection involved in formation of intestinal air-breathing function in M. anguillicaudatus. This is the first report of developmental transcriptome of posterior intestine in M. anguillicaudatus, offering a substantial contribution to the sequence resources for this species and providing a deep insight into the formation mechanism of its intestinal air-breathing function. This report demonstrates that M. anguillicaudatus is a good model for studies to identify and characterize the molecular basis of accessory air-breathing organ development in fish.

show abstract

Section: Discussionmentioning

confidence: 53%

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

Luo

Cao

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Thus far, massive gene expression analyses addressing clock-driven transcription in fish larvae have mostly been conducted in zebrafish 2 , 3 . Both microarray and RNA-Seq gene expression profiling of whole-body larvae of other teleostean fishes have been used to unravel key issues of development 4 , 5 , domestication 6 , and the effects of different environmental factors such as pollutants, diet, stress, and infection 7 – 12 but not to elucidate overall daily transcriptomic organization.…”

Section: Introductionmentioning

confidence: 99%

The circadian transcriptome of marine fish (Sparus aurata) larvae reveals highly synchronized biological processes at the whole organism level

Yúfera

Perera

Mata-Sotres

et al. 2017

Sci Rep

View full text Add to dashboard Cite

The regulation of circadian gene expression remains largely unknown in farmed fish larvae. In this study, a high-density oligonucleotide microarray was used to examine the daily expression of 13,939 unique genes in whole gilthead sea bream (Sparus aurata) larvae with fast growth potentiality. Up to 2,229 genes were differentially expressed, and the first two components of Principal Component Analysis explained more than 81% of the total variance. Clustering analysis of differentially expressed genes identified 4 major clusters that were triggered sequentially, with a maximum expression at 0 h, 3 h, 9–15 h and 18-21 h zeitgeber time. Various core clock genes (per1, per2, per3, bmal1, cry1, cry2, clock) were identified in clusters 1–3, and their expression was significantly correlated with several genes in each cluster. Functional analysis revealed a daily consecutive activation of canonical pathways related to phototransduction, intermediary metabolism, development, chromatin remodeling, and cell cycle regulation. This daily transcriptome of whole larvae resembles a cell cycle (G1/S, G2/M, and M/G1 transitions) in synchronization with multicellular processes, such as neuromuscular development. This study supports that the actively feeding fish larval transcriptome is temporally organized in a 24-h cycle, likely for maximizing growth and development.

show abstract

“…In European sea bass, massive gene expression analysis have undertaken for gills, liver, brain, eggs, and larvae (Geay et al, 2011; Magnanou et al, 2014; Nuñez Ortiz et al, 2014; Kaitetzidou et al, 2015). A high-quality chromosome-scale genome assembly is also available (Tine et al, 2014) for this species, but in-depth analysis of the intestinal transcriptome remains to be fully addressed.…”

Section: Introductionmentioning

confidence: 99%

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

2016

View full text Add to dashboard Cite

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.

show abstract

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

Abstract: Kaitetzidou E, Xiang J, Antonopoulou E, Tsigenopoulos CS, Sarropoulou E. Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax).

Cited by 20 publications

References 98 publications

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

The circadian transcriptome of marine fish (Sparus aurata) larvae reveals highly synchronized biological processes at the whole organism level

Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

Contact Info

Product

Resources

About