Sequencing and characterization of the transcriptome of half-smooth tongue sole (Cynoglossus semilaevis)

Abstract

BackgroundHalf-smooth tongue sole (Cynoglossus semilaevis) is a valuable fish for aquaculture in China. This fish exhibits sexual dimorphism, particularly different growth rates and body sizes between two genders. Thus, C. semilaevis is a good model that can be used to investigate mechanisms responsible for such dimorphism, this model can also be utilized to answer fundamental questions in evolution and applied fields of aquaculture. Hence, advances in second-generation sequencing technology, such as 454 pyrosequencing, could provide a robust tool to study the genome characteristics of non-model species.ResultsIn this study, C. semilaevis was subjected to de novo transcriptome sequencing and characterization. A total of 749,954 reads were generated using a single 454 sequencing run in a full PicoTiter plate. These reads were then assembled into 62,632 contigs with a 10-fold average sequencing coverage. A total of 26,589 sequences were successfully annotated based on sequence similarities; among these sequences, 3,451 transcripts exhibited gene ontology terms and 2,362 showed enzyme commissions associated with 186 pathways from Kyoto Encyclopedia of Gene and Genomes pathways. A search of repetitive elements was performed, and 1,898 transposable elements were identified. Approximately 7,800 simple-sequence repeats and 21,234 single-nucleotide polymorphisms were also detected.ConclusionsOur data provided an integrated and comprehensive transcriptome resource for C. semilaevis. These data could be used for further research in population genetics, gene function, and tissue-specific gene expressions.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-470) contains supplementary material, which is available to authorized users.

Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae)

“…This type of retrotransposon, have been extensively characterized and are abundant in animals and plants (Ferreira et al 2011) as well as in fish genomes (Poulter and Butler 1998;Volff et al 2001Volff et al , 2003Wang et al 2014). The origin of these elements can be traced back prior to vertebrates differentiation (Volff et al 2003).…”

“…Schartl et al (2013) through NGS approach in other viviparous Cyprinodontiformes, X. maculatus, found that 4.8 % of the transcriptome was derived from TE sequences representing about 40 different families, indicating that many of the platyfish TEs are most likely still active. The most active TEs were the Tc1 DNA transposons.In a recent transcriptome analysis of the Cynoglossus semilaevis fish, Wang et al (2014) found that among 1898 sequences containing TEs, 904 were retroelements and 994 transposons. In the last genomic fraction, the most represented were hAT (13.2 %), and Tc1-Mariner (12.5 %) elements, suggesting that DNA transposon elements could be also distinctly distributed among fish groups.…”

Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection

“…55,335 unigenes failed comparing to any database, 80% sequences of unigenes which failed to be annotated were short than 300 nt. 38,337 putative open reading frames, larger than 50 amino acids, have been detected in the transcriptome dataset. To assign functional information to transcripts, 39,281 genes were selected for annotation with the GO database by GOminer [45].…”

“…Previous reports on immune analysis in C. semilaevis are concentrated on single gene, such as TLR9 [31], Interleukin-8 [32], chemokines such as CsCXCe1 [33] and CsCCK1 [34], MHC IIA and IIB [35] and goose-type lysozyme [36]. Although the whole genome reference [37] and some transcriptome information in C. semilaevis are now available [38], the understanding of the molecular mechanism against V. anguillarum infection is still deficient, thereby it is difficult to establish the measures to control the V. anguillarum disease. In practice, two phenotypes had been observed in the C. semilaevis domestic population after V. anguillarum infection.…”

Duplicated major histocompatibility complex class II genes in the tongue sole (Cynoglossus semilaevis)

“…These studies have shown that tongue sole shares characteristics with Japanese flounder ( Paralichthys olivaceus ) and turbot ( Scophthalmus maximus ), which reinforce the close relationships among these Pleuronectiformes fishes. In addition, recent studies in the tongue sole transcriptome (Wang et al., ) and genome (Chen et al., ) have identified the unique molecular characteristics that underline its adaption to a benthic lifestyle.…”