Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain

Zhang, Ju; Karsi, Attila; Kocabas, Arif; Patterson, Andrea; Li, Ping; Cao, Dongfeng; Dunham, Rex A.; Liu, Zhanjiang

doi:10.1016/s0378-1119(00)00491-1

Cited by 99 publications

(53 citation statements)

References 25 publications

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“…Matches were considered to be significant only when the probability (P) was less than 10 − 4 . The DNA sequences matched with known or predicted genes were categorized into different functional groups according to categories described by Ju et al (2000). The predications of ORF were done by using ORF Finder, which were from the web site http://www.ncbi.nlm.nih.gov.…”

Section: Plasmid Preparation and Sequencing Analysismentioning

confidence: 99%

“…The 181 known genes were categorized into 15 groups according to categories described by Ju et al (2000). Among the known genes, the genes homologous to known sequences of unknown functions are the largest group, which accounts for 12.8%.…”

Section: Functional Categorization Of the Known Genesmentioning

confidence: 99%

“…Expressed sequence tags (ESTs) are the basis for functional genomic research because they give a first glimpse of transcription profiles in specific tissue (Ju et al, 2000). Careful analyses of the sequence data can further provide significantly functional, structural and evolutionary information (Quackenbush et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

“…Currently, a lot of fish ESTs have been released from model fish and food fish species, but over 50% of the teleost ESTs were generated from model fish, such as zebrafish (Gong, 1999), medaka , and fugu (Jaillon et al, 2004). Only a few of specific tissues have become the object of EST projects from some aquaculture species, such as winter flounder (Douglas et al, 1999), Japanese flounder (Inoue et al, 1997), salmon (Davey et al, 2001;Martin et al, 2002), channel catfish (Karsi et al, 1998Ju et al, 2000;Kim et al, 2000;Kocabas et al, 2002), red sea bream (Chen et al, 2004), tilapia (Shiue et al, 2004), common carp (Kono et al, 2004), and gilthead sea bream (Sarropoulou et al, 2005). The lack of EST resources in commercial fish species prohibits use of modern functional genomic approaches for the study of growth, development, reproduction, stress biology and molecular breeding (Chen et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

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EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

et al. 2006

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Section: Plasmid Preparation and Sequencing Analysismentioning

confidence: 99%

Section: Functional Categorization Of the Known Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

et al. 2006

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“…These sequence data are useful resource for further studies in the endangerous fish species, especially in species conservation, reproduction, growth, molecular biology and genetics. Expressed sequence tags (ESTs) analysis is an efficient approach to identify new genes and to profile gene expression in tissues or cells [23][24][25][26]. EST information can provide significant functional, structural and evolutionary information [27], and can also be used in many other applications, such as the discovery of molecular markers [28][29][30] and the detection of gene loci that influence a quantitative trait locus (QTL) of growth and reproduction [31][32][33] Recently, fish EST sequence resources are rapidly growing in molecular databases, but no EST data have been reported from any sturgeon species.…”

Section: Discussionmentioning

confidence: 99%

EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, Acipenser sinensis

Cao

Leng

et al. 2011

Mol Biol Rep

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Chinese sturgeon (Acipenser sinensis) is a rare and endangered species and also an important resource for the sturgeon aquaculture industry, however, a few genes have been identified in this species. We report here construction of a pituitary cDNA library from a 24 years old female Chinese sturgeon just after its spawning, and obtained 2,025 ESTs from the library. 885 unique sequences were identified, which were categorized into 12 functional groups. More than half of the unique sequences (57%) do not match with annotated sequences in the public databases. Three of these novel genes were further identified. Notably, a full-length of cDNA (1,143 bp) encoding somatolactin of 232 amino acids was identified. Phylogenetic analysis showed 97% amino acid identity with White sturgeon somatolactin. RT-PCR analysis indicated that the somatolactin mRNA was only detected in pituitary. Pituitary-specific expression of the somatolactin suggested that the protein may play important physiological functions in pituitary-endocrine system of the Chinese sturgeon.

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Transcriptome Characterization Through the Analysis of Expressed Sequence Tags

Liu¹

2007

Aquaculture Genome Technologies

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Sequencing of expressed sequence tags (ESTs) has been one of the primary techniques used for transcriptome analysis in a wide spectrum of species including those utilized for aquaculture. However, many researchers are still unfamiliar with the many genome applications and byproducts of EST analysis, and they often regard ESTs as only short random sequences. Additionally, lack of cDNA library normalization, project planning, and quality control have often restricted the value of EST resources created in many laboratories. This review aims to address these issues by providing information on the construction of normalized cDNA libraries for efficient generation and analysis of ESTs and by highlighting the significance of EST analysis for the genome research of species lacking a sequenced genome. A successful EST project can provide the sequence tools needed for not only gene discovery, but also for physical, linkage and comparative mapping, analysis of alternative splicing and gene duplication, and microarray development.* This paper is dedicated to the late Professor Dr. Boaz Moav who was not only a great friend, mentor and colleague, but also a role model for the author to work relentlessly for scientific discoveries since 1988.

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Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain

Cited by 99 publications

References 25 publications

EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

EST-based identification of genes expressed in the hypothalamus of male orange-spotted grouper (Epinephelus coioides)

EST dataset of pituitary and identification of somatolactin and novel genes in Chinese sturgeon, Acipenser sinensis

Transcriptome Characterization Through the Analysis of Expressed Sequence Tags

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