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

Li, Ping; Peatman, Eric; Wang, Shaolin; Feng, Jinian; He, Chongbo; Baoprasertkul, Puttharat; Xu, Peng; Kucuktas, Huseyin; Nandi, Samiran; Somridhivej, Benjaporn; Serapion, Jerry; Simmons, Micah; Turan, Cemal; Liu, Lei; Muir, William M.; Dunham, Rex A.; Brady, Yolanda J.; Grizzle, John M.; Liu, Zhanjiang

doi:10.1186/1471-2164-8-177

Cited by 73 publications

(41 citation statements)

References 49 publications

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“…The conservation of marker/ gene positions was the highest between catfish and zebrafish, consistent with their phylogenetic relationships (Xu et al 2006;Steinke et al 2006). The overall annotation rate of the 331 mapped ESTs was lower than that of the average ESTs (.50%; Li et al 2007), largely because of the location of microsatellites being associated mostly with 59-or 39-UTRs.…”

Section: Identification Of Potentially Conserved Synteniesmentioning

confidence: 53%

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Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

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Section: Identification Of Potentially Conserved Synteniesmentioning

confidence: 53%

“…Liu, unpublished data), understanding of the genomic architecture (Liu et al 1998;Liu 2007;Nandi et al 2007), and a large number of ESTs ( Ju et al 2000;Cao et al 2001;Karsi et al 2002;Kocabas et al 2002;Li et al 2007). However, these genome resources are as yet nonintegrated and thus underutilized due to the lack of a platform for comparative genome analysis.…”

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confidence: 99%

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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“…On the other hand, a rapid development of genetic and genomics resources has been made recently for economically important aquacultured fish species such as channel catfish (Li et al 2007;Xu et al 2007) rainbow trout (Rexroad III et al 2003;Govoroun et al 2006), Atlantic salmon (Thorsen et al 2005;Davidson et al 2010), Atlantic cod (Gadus morhua) (Nielsen et al 2006;Wesmajervi et al 2007;Johansen et al 2009) and Gilthead sea bream (Sparus aurata) Senger et al 2006;Sarropoulou et al2007). …”

Section: Genomic and Genetic Resources Of Zebrafish And Other Aquaculmentioning

confidence: 98%

“…Genetic resources for catfish include over 500,000 ESTs Li et al 2007), over 10,000 full-length cDNA (Chen et al 2010), over 300,000 putative SNPs , and the development of high-density SNP chip is in progress (Lu et al 2010). In Atlantic Cod 724 putative SNP developed from 17,056 EST were evaluated, from which 318 segregating SNPs were selected for future genetic analysis (Moen et al 2008b).…”

Section: Genomic and Genetic Resources Of Zebrafish And Other Aquaculmentioning

confidence: 99%

Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

Ulloa

Iturra

Neira

et al. 2011

Rev Fish Biol Fisheries

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Zebrafish (Danio rerio) is a common research model in fish studies of toxicology, developmental biology, neurobiology and molecular genetics; it has been proposed as a possible model organism for nutrition and growth studies in fish. The advantages of working with zebrafish in these areas are their small size, short generation time (12-14 weeks) and their capacity to produce numerous eggs (100-200 eggs/clutch). Since a wide variety of molecular tools and information are available for genomic analysis, zebrafish has also been proposed as a model for nutritional genomic studies in fish. The detailed study of every species employed as a model organism is important because these species are used to generalize how several biological processes occur in related organisms, and contribute considerably toward improving our understanding of the mechanisms involved in nutrition and growth. The objective of this review is to show the relevant aspects of the nutrition and growth in zebrafish that support its utility as a model organism for nutritional genomics studies. We made a particular emphasis that gene expression and genetic variants in response to zebrafish nutrition will shed light on similar processes in aquacultured fish.

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“…Based on the cDNA sequences of L-type lectin from zebrafish, we searched the channel catfish expressed sequence tags (ESTs) database [30,31] in NCBI using BLAST. The clone CBPN21042 (GenBank ID: FD339357.1 and FD339356.1), CBPN25640 (GenBank ID: FD345714.1 and FD345715.1) and CBPO11108 (GenBank ID: FD041401.1 and FD041402.1) were determined to encode the putative complete cDNAs of catfish ERGIC-53, VIP36, and VIP36-like genes.…”

Section: Identification and Sequencing Of Catfish L-type Lectin Cdnasmentioning

confidence: 99%

Molecular characterization of three L-type lectin genes from channel catfish, Ictalurus punctatus and their responses to Edwardsiella ictaluri challenge

Zhang

Peatman

Liu

et al. 2012

Fish & Shellfish Immunology

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

Cited by 73 publications

References 49 publications

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

Molecular characterization of three L-type lectin genes from channel catfish, Ictalurus punctatus and their responses to Edwardsiella ictaluri challenge

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