Plant & Animal Genome IX Conference

Poster: Sequencing & EST
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SEQUENCING, COMPARATIVE ANALYSIS AND IN SILICO MAPPING OF 12,614 ESTs FROM NORMALIZED AND SUBTRACTED CATTLE PLACENTA cDNA LIBRARIES

¹ W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 340 Edward R. Madigan Laboratory, 1201 W. Gregory Drive, Urbana, IL 61801, USA

² The University of Iowa, 451 Eckstein Medical Research Building, Iowa City, IA 52242, USA

EST sequencing of a normalized cattle placenta cDNA library was conducted in two stages. First, high throughput DNA sequencing was performed on the normalized library resulting in the deposit of 4886 high quality filtered and trimmed ESTs into GenBank. Following a redundancy analysis, PCR products from approximately 8100 cattle cDNA clones were pooled for serial subtraction of the normalized placenta cDNA library. Following subtraction, high throughput sequencing, trimming and quality analysis, 7728 additional high quality ESTs were submitted to GenBank. A total of 2888 sequence clusters and 4359 singlets were identified using PHRAP, for a total of 7247 unique sequences. Thus, overall redundancy among the 12,614 placenta ESTs was 42.5%. The ESTs were subjected to comparative analysis and in silico mapping using a new web-based tool for executing COMPASS (comparative mapping by annotation and sequence similarity, see Rebeiz and Lewin Animal Biotechnol. 11:75, 2000). The results were used to select genes for filling gaps on the cattle-human whole genome comparative map (Band et al., Genome Research 10:1369, 2000)and for creating a 3800 gene cattle microarray for functional genomic studies (see Band et al., this meeting). The ESTs and associated annotation were generated as part of USDA-NRI resource grant AG 99-35205-8534.