Sequence evaluation of four pooled-tissue normalized bovine cDNA librariesand construction of a gene index for cattle

An essential component of functional genomics studies is the sequence of DN A expressed in tissues of interest. To provide a resource of bovine-specifi c expressed sequence data and facilitate this powerful approach in cattle r esearch, four normalized cDNA libraries were produced and arrayed for high- throughput sequencing. The libraries were made with RNA pooled from multipl e tissues to increase efficiency of normalization and maximize the number o f independent genes for which sequence data were obtained. Target tissues i ncluded those with highest likelihood to have impact on production paramete rs of animal health, growth, reproductive efficiency, and carcass merit. Su ccess of normalization and inter- and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 tot al sequences deposited in GenBank). Sequence comparison and assembly of the se sequences was performed in combination with 56,500 other bovine EST sequ ences present in the GenBank dbEST database to construct a cattle Gene Inde x (available from The Institute For Genomic Research at http://www.tigr.org /tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the We b site. Analysis of individual library sequence data indicates that the poo led-tissue approach was highly effective in preparing libraries for efficie nt deep sequencing.