De novo assembly and comprehensive characterization of the skeletal muscle transcriptomes of the European anchovy (Engraulis encrasicolus)

Eldem, Vahap; Zararsız, Gökmen; Erkan, Melike; Bakır, Yakup

doi:10.1016/j.margen.2015.01.001

Cited by 6 publications

(3 citation statements)

References 14 publications

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“…FastQC generates a HTML output containing a number of graphical illustrations providing the number and length of raw reads and duplication rate, but two main component of the FastQC tool: (i) per base sequence content and (ii) per base sequence quality are particularly useful in guiding pre-processing step. The most popular pre-processing tools are FASTX-Toolkit [15], Trimmomatic [16], Cutadapt [17], NGS QC Toolkit [18] and Qtrim [19], and regardless of the tools used, common pre-processing steps include: (i) removing adapter sequences, (ii) discarding the low quality reads (Q ≤ 20) and ambiguous nucleotides (Ns), (iii) removing the short-read length sequences (length below 50 base pair (bp)) and (iv) trimming low quality bases at the both ends of reads (generally irst 10 bp) (Figure 1) [20]. After pre-processing, resulting high-quality reads are ready for downstream analysis; de novo transcriptome assembly.…”

Section: Quality Check and Pre-processing Of Raw Readsmentioning

confidence: 99%

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Eldem¹,

Zararsız²,

Taşçi³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq-based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for de novo transcriptome assemblies, (v) approaches for transcript abundance and diferential expression estimations and inally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects.

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Section: Quality Check and Pre-processing Of Raw Readsmentioning

confidence: 99%

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Eldem¹,

Zararsız²,

Taşçi³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

Self Cite

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“…The skeletal muscle of fish accounts for 40% to 50% of its body weight. Muscle growth requires the proliferation and differentiation of myoblasts, and the quality of skeletal muscle has an important impact on an individual's development (Eldem et al, 2015; Wang et al, 2020). Muscle growth is regulated by various factors or mechanisms, such as myostatin, insulin‐like growth factors (IGFs) and growth hormone (GH).…”

Section: Introductionmentioning

confidence: 99%

“…Muscle growth requires the proliferation and differentiation of myoblasts, and the quality of skeletal muscle has an important impact on an individual's development (Eldem et al, 2015;Wang et al, 2020).…”

mentioning

confidence: 99%

Comparative transcriptome analysis of mixed tissues of black porgy ( Acanthopagrus schlegelii ) with differing growth rates

Lin

Zhang

Solberg

et al. 2021

Aquaculture Research

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Black porgy (Acanthopagrus schlegelii) belongs to the order Perciformes, the family Sparidae and the genus Acanthopagrus. It is an essential marine aquaculture fish, with an oblong and flat body and holds the characteristics of fast growth, good meat quality, strong disease resistance and strong adaptability to various environments (Zhu & Zhu, 2014). Fish growth traits refer to the growth-related traits such as body weight, body length, head length, body width, body height and tail stalk length of individual fish. The faster the fish grow, the less time is needed for breeding until market size, the lower the economic cost and the higher the yield at harvest, which can be beneficial for meeting market demands, and increase the economic and ecological benefits of fish breeding (Yin et al., 2020). Therefore, growth traits are not only one of the economic traits that best reflects the growth status of the fish, but it is also a very important reference indicator for the development of fish farming. With the development of aquaculture, the research on growth traits has received more and more attention.

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De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864)

et al. 2017

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To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Relative expression of liver genes between diploid and triploid bighead catfish revealed more than 90% of the annotated unigenes similarly expressed, regardless of ploidy, whereas 362 upregulated and 83 downregulated with at least a twofold change in triploid relative to diploid. Quantitative real-time PCR of 15 differentially expressed growth-related genes showed consistency between the expression profiles of those genes with the results from RNA-seq analysis. Our results showed that genes in C. macrocephalus liver responded independently to triploidy with the majority showing similar expression levels between diploid and triploid (a dosage compensation phenomenon). The underlying mechanism of the varying gene expression patterns was discussed. Notably, 5 of the top 20 upregulated genes associated with stress response and thus may reflect stress caused by triploidy. The present study adds a substantial contribution to the sequence data available for C. macrocephalus and hence provides valuable resources for further studies. Furthermore, it gives information that may enhance understanding of triploid physiology.

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De novo assembly and comprehensive characterization of the skeletal muscle transcriptomes of the European anchovy (Engraulis encrasicolus)

Cited by 6 publications

References 14 publications

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Comparative transcriptome analysis of mixed tissues of black porgy ( Acanthopagrus schlegelii ) with differing growth rates

De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864)

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