Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Workshop: Aquaculture
Catfish is the major aquaculture species in the US. Genome research in catfish requires genomic resources such as large numbers of expressed sequence tags (ESTs). We have developed a series of cDNA libraries from various tissues including head kidney, spleen, liver, skin, brain, stomach, intestine, ovary, olfactory tissue, gill, muscle, testis, pituitary, eye, and trunk kidney. As part of the catfish transcriptome analysis, we have analyzed 2,228 EST clones from the head kidney library, 1,201 clones from the brain library, 1,909 clones from the skin library, 1,500 clones from the spleen library, and 1,091 clones from the liver library. Expression profiling indicated that gene expression in several tissues is highly polarized with a small number of genes being expressed at high levels. Our long and clean sequences generated from the LI-COR automatic sequencers allowed identification of genes for large proportions of all the sequenced clones. Repeated sequencing, a negative element for large-scale EST analysis, has been exploited for identification of single nucleotide polymorphism (SNP) markers and systematic analysis of highly expressed genes. In this later effort, we have characterized all the 32 ribosomal proteins involved in the 40S ribosome and all the 47 ribosomal proteins involved in the 60S ribosome. In addition, alternatively spliced and alternatively polyadenylated transcripts were identified. Microarray techniques were used to identify differentially expressed genes under stressful conditions. These resources set the foundation for functional genomic and comparative genomic research in aquaculture species.