Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach

Cam, Aurélie Le; Bobe, Julien; Bouchez, Olivier; Cabau, Cédric; Kah, Olivier; Klopp, Christophe; Lareyre, Jean‐Jacques; Guen, Isabelle Le; Lluch, Jérôme; Montfort, Jérôme; Moreews, François; Nicol, Barbara; Prunet, Patrick; Rescan, Pierre‐Yves; Servili, Arianna; Guiguen, Yann

doi:10.1016/j.gene.2012.03.053

Cited by 9 publications

(2 citation statements)

References 61 publications

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“…With the advent of the next generation sequencing technologies, the gathering of large amounts of sequence data for a given organism at affordable costs is more feasible [12], and high-throughput 454 pyrosequencing has been used to explore the transcriptome of rainbow trout ( Oncorhynchus mykiss ) [13,14], Atlantic cod ( Gadus morhua ) [15] and turbot [16]. In the case of gilthead sea bream, two deep sequencing studies have been reported from whole larval tissues [17] and skeletal muscle [18], yielding 68,289 and 43,461 assembled sequences, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…As the annotation success of a sequencing project is highly dependent on the size of the assembled sequences, approaches conducted to obtain longer sequences become desirable. At this respect, it has been proved in some animal models, including rainbow trout [13,14], that the use of two or more tissues for sequencing and assembly increases the number of annotated genes. On this basis, the primary goal of the present study was to generate a large amount of gilthead sea bream transcriptomic reads from metabolically and immunologically relevant tissues by means of the construction of five 454 pyrosequencing libraries, combining them with Sanger sequences from public repositories and our own published data.…”

Section: Introductionmentioning

confidence: 99%

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Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts

et al. 2013

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BackgroundThe gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1).ResultsSequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts.ConclusionsThe newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts

et al. 2013

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Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, Annotation and Marker Discovery

Chen

Liu

et al. 2014

Mol Biol Rep

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The ridgetail white prawn Exopalaemon carinicauda is one of major economic mariculture species in eastern China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its good traits. In the present study, 454 pyrosequencing was undertaken to investigate the transcriptome profiles of E. carinicauda. A collection of 1,028,710 sequence reads (459.59 Mb) obtained from cDNA prepared from eyestalk and hemocytes was assembled into 162,056 expressed sequence tags (ESTs). Of these, 29.88 % of 48,428 contigs and 70.12 % of 113,628 singlets possessed high similarities to sequences in the GenBank non-redundant database, with most significant (E value <1e(-10)) unigenes matches occurring with crustacean and insect sequences. KEGG analysis of unigenes identified putative members of biological pathways related to growth and immunity. In addition, we obtained a total of putative 125,112 SNPs and 13,467 microsatellites. These results will contribute to the understanding of the genome makeup and provide useful information for future functional genomic research in E. carinicauda.

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Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus

Xiao

Bao

Zhao

et al. 2019

J Genet

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Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach

Cited by 9 publications

References 61 publications

Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts

Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts

Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, Annotation and Marker Discovery

Transcriptome sequencing and de novo analysis of the northern snakehead, Ophiocephalus argus

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