PAG-X  Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

A PIG REPRODUCTION EST PROJECT: DEVELOPMENT OF EST SEQUENCE DATA AND MAP LOCATIONS FOR GENES EXPRESSED IN MAJOR FEMALE REPRODUCTIVE TISSUES

Chrisopher K Tuggle1 , Jon A Green2 , Carolyn Fitzsimmons1 , Rami Woods2 , Randall S Prather2 , Sergei Malchenko3 , M. Bento Soares3 , Chad A Roberts4 , Kevin Pedretti4 , Thomas Casavant4

1 Department of Animal Science, Iowa State University, 2255 Kildee Hall Ames, IA 50011
2 Department of Animal Science, 162 ASRC University of Missouri-Columbia, Columbia, MO 65211
3 Department of Pediatrics, University of Iowa, 451 Eckstein Medical Research Building, Iowa City, IA 52242
4 Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242
5 Department of Animal Science, University of Nebraska, Lincoln, NE 68583

A consortium of five institutions is developing extensive expressed sequence and mapping data for cDNAs expressed in major female reproductive tissues. We have produced 20 libraries from different stages of estrus or gestation for whole embryo, anterior pituitary, hypothalamus, ovary, uterus, and term placenta. The anterior pituitary, placenta and uterine libraries have been normalized. A total of 14,602 sequences from random clones has been produced and submitted to Genbank. The average read length across this dataset is >400 base pairs. As assessed by clustering analysis, these data represent 8,859 different genes. A BLAST analysis indicates that 4,405 of these clusters are unique relative to existing porcine Genbank genes and ESTs (BLAST score <50). To facilitate selection of genes for comparative mapping, we have developed software to predict the cytogenetic location of pig ESTs. We identified human loci with a BLAST score >200 to our EST dataset, and then predicted the pig location of high-scoring ESTs based on human cytogenetic and RH mapping data, along with human:pig chromosome painting information. Pig EST matches to human loci with consistent cytogenetic and RH mapping locations total 1,486. Within the human genome, there is an average distance of 9.4±5.8 cR between loci with a pig EST match. On average, there is 20.9±3.8 RH-mapped genes between each human loci matched to a pig EST. To date, 50 loci have been mapped using both the SCHP and the RH panel. A WWW site has been established for access to these sequences and the analysis data (http://pigest.genome.iastate.edu).

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