Transcriptome of channel catfish (<i>Ictalurus punctatus</i>): initial analysis of genes and expression profiles of the head kidney

Cao, Dongfeng; Kocabas, Arif; Zhang, Ju; Karsi, Attila; Li, P.; Patterson, Andrea; Liu, Z.

doi:10.1046/j.1365-2052.2001.00753.x

Cited by 64 publications

(28 citation statements)

References 18 publications

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“…These cDNA libraries were sequenced to generate the 31,215 ESTs reported here. Two of these libraries (channel catfish head kidney and spleen) have been previously reported [27,28], but were sequenced at greater depths in this project. Twelve of the cDNA libraries were produced from channel catfish tissues, and five from blue catfish tissues.…”

Section: Resultsmentioning

confidence: 99%

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Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

Peatman

Wang

et al. 2007

BMC Genomics

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Background: EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish.

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Section: Resultsmentioning

confidence: 99%

“…Initial sequencing of four catfish cDNA libraries, channel catfish brain, head kidney, skin, and spleen, was previously reported [27,28,44,45]. Fifteen additional libraries from the tissues listed above were constructed here closely following protocols used previously.…”

Section: Methodsmentioning

confidence: 99%

Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

Peatman

Wang

et al. 2007

BMC Genomics

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“…It also produces markers and resources for the development of cDNA microarrays [13]. In catfish, over 11 000 ESTs have been sequenced and deposited in GenBank [1,4,5,6,11]. The Institute of Genome Research (TIGR) has constructed a gene index that includes 5905 unique sequences (http://www.tigr.org).…”

Section: Development Of Genomic Resourcesmentioning

confidence: 99%

“…To date, one genomic λ DNA library has been made [8,10] [1], spleen [11], skin [5], liver, brain [4], stomach, intestine, ovary, gill, muscle, testis, pituitary [6], olfactory tissue, and trunk kidney (posterior kidney); 14 of the 15 cDNA libraries were made in the pSport-1 vector (Life Technologies, MD) and one was made in the λ Unizap cloning vector (Stratagene, CA). In consideration of their uses for the identification of SNPs, tissues from 15 fish were used; as genomic resources to include potentially most, if not all, transcripts for the study of disease-related genes, tissues were collected from both healthy and infected fish at various times after infection.…”

Section: Development Of Genomic Resourcesmentioning

confidence: 99%

A review of catfish genomics: progress and perspectives

Liu

2003

Comp Funct Genom

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Catfish is one of the lower teleosts whose genome research is important for evolutionary genomics. As the major aquaculture species in the USA, its genome research also has practical and economical implications. Much progress has been made in recent years, including the development of large numbers of molecular markers, the construction of framework genetic linkage maps, the identification of putative markers involved in performance traits, and the development of genomic resources. Repetitive elements have been identified and characterized in the catfish genome that should facilitate physical analysis of the catfish genome. A large number of genes or full-length cDNAs have been analysed using genomic approaches, providing information on gene structure, gene evolution and gene expression in relation to functions. Catfish genome research has come to a stage when physical mapping through BAC contig construction is greatly demanded, in order to develop regional markers for QTL analysis and for large-scale comparative mapping. The current effort in large-scale EST analysis and type I marker mapping should further enhance research efficiency through comparative mapping. Candidate gene identification is being accelerated through the use of cDNA microarrays.

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“…However, the repeat structures of the channel catfish genome have not been well studied, particularly the interspersed types of repeats. Ongoing projects in the areas of linkage and physical mapping (Liu et al 2003) and genomic and expressed sequence tag (EST) sequencing (Cao et al 2001;Kocabas et al 2002) will benefit from an assessment of the prevalent Tc1 transposable elements in catfish, allowing for accurate processing, annotation, and assessment of sequences and accurate assembly of genetic maps. Therefore, here we assessed the distribution and diversity of Tc1 elements in the channel catfish genome as well as evaluating the extent of transcription of Tc1 transposases.…”

Section: Introductionmentioning

confidence: 99%

Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)

Nandi

Peatman

et al. 2006

Genetica

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We have assessed the distribution and diversity of members of the Tc1/mariner superfamily of transposable elements in the channel catfish (Ictalurus punctatus) genome as well as evaluating the extent of transcription of Tc1 transposases in the species. Through use of PCR amplification and sequencing, assessment of random BAC end sequences (BES) equivalent to 1.2% genome coverage, and screening of over 45,000 catfish ESTs, a significant proportion of Tc1-like elements and their associated transcripts were captured. Up to 4.2% of the catfish genome in base pairs appears to be composed of Tc1-like transposon-related sequences and a significant fraction of the catfish cellular mRNA, approximately 0.6%, was transcribed from transposon-related sequences in both sense and antisense orientations. Based on results of repeat-masking, as much as 10% of BAC end sequences from catfish, which is a random survey of the genome, contain some remnant of Tc1 elements, suggesting that these elements are present in the catfish genome as numerous, small remnants of the transposons. Phylogenetic analysis allowed comparison of catfish Tc1 transposase types with those found in other vertebrate and invertebrate species. In spite of the existence of many types of Tc1-like sequences that are not yet able to be placed in clades with strong statistical support, it is clear that multiple families of Tc1-like elements exist in channel catfish.

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Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney

Cited by 64 publications

References 18 publications

Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

A review of catfish genomics: progress and perspectives

Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)

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