ArticleBMC genomics2010
Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 3 of them syntheses that pooled it.
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Who cites it
83 citing papers in PubMed, 3 syntheses or guidelines pooled it, 145 citations in OpenAlex.
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- De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.Genetica · 2022Article
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- Comprehensive Characterization of Circular RNAs in Ovary and Testis From Nile Tilapia.Frontiers in veterinary science · 2022Article
- Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis.Fish physiology and biochemistry · 2021Article
- Expression and characterization of rainbow trout Oncorhynchus mykiss recombinant myoglobin.Fish physiology and biochemistry · 2021Article
- Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach (Biology · 2021Article
- Isolation and characterization of SNP markers of rainbow trout (Onchorhynchus mykiss Walbaum, 1792) from transcriptomic sequences.Molecular biology reports · 2021Article
- PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.Frontiers in genetics · 2021Article
- Article
- RNA-Seq-based transcriptome analysis of reproduction- and growth-related genes in Lateolabrax japonicus ovaries at four different ages.Molecular biology reports · 2018Article
- Identification of genes involved in gonadal sex differentiation and the dimorphic expression pattern in Takifugu rubripes gonad at the early stage of sex differentiation.Fish physiology and biochemistry · 2018Article
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- Immunomodulatory Effects of Dietary Seaweeds in LPS Challenged Atlantic SalmonFrontiers in physiology · 2018Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evolutionary biology. However, to date there is no genome reference sequence to facilitate the development of molecular technologies that utilize high-throughput characterizations of gene expression and genetic variation. Alternatively, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation.
resultsHigh-throughput deep sequencing of the Swanson rainbow trout doubled-haploid transcriptome using 454-pyrosequencing technology yielded ~1.3 million reads with an average length of 344 bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus (TC) sequences (average length of 662 bp) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing sequences resulted in 161,818 TCs (average length of 758 bp) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed high similarities to transcriptomes of other fish species with known genome sequences.
conclusionThe 454 library significantly increased the suite of ESTs available for rainbow trout, allowing improved assembly and annotation of the transcriptome. Furthermore, the 454 sequencing enables functional genome research in rainbow trout, providing a wealth of sequence data to serve as a reference transcriptome for future studies including identification of paralogous sequences and/or allelic variation, digital gene expression and proteomic research.
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