BMC Genomics 2004, 5:54 http://www.biomedcentral.com/1471-2164/5/54 Table 2: EST summary and assembly results. cDNA clones sequenced high-quality sequences mt DNA sequence seqs submitted to NCBI sequences assembled PaCE clusters ESTs in contigs contigs singlets putative transcripts aIncludes 16,030 ESTs from [20]. A. mex 21830 19383 2522 16861 32891a 11381 25457 3756 7434 11190 A. t. tig 24234 20599 1223 19376 19376 10226 12676 3201 6700 9901 primarily from regenerating larval tissues in A. mexicanum and several non-regenerating larval tissues in A. t. tigrinum. EST sequencing and clustering A total of 46,064 cDNA clones were sequenced, yielding 39,982 high quality sequences for A. mexicanum and A. t. tigrinum (Table 2). Of these, 3,745 corresponded to mtDNA and were removed from the dataset; complete mtDNA genome data for these and other ambystomatid species will be reported elsewhere. The remaining nuclear ESTs for each species were clustered and assembled sepa- rately. We included in our A. mexicanum assembly an additional 16,030 high quality ESTs that were generated recently for regenerating tail and neurula stage embryos [20]. Thus, a total of 32,891 and 19,376 ESTs were clustered for A. mexicanum and A. t. tigrinum, respectively. Using PaCE clustering and CAP3 assembly, a similar number of EST clusters and contigs were identified for each species (Table 2). Overall contig totals were 11,190 and 9,901 for A. mexicanum and A. t. tigrinum respectively. Thus, although 13,515 more A. mexicanum ESTs were assembled, a roughly equivalent number of contigs were obtained for both species. This indicates that EST develop- ment was more efficient for A. t. tigrinum, presumably because ESTs were obtained primarily from the normal- ized AG library; indeed, there were approximately twice as many ESTs on average per A. mexicanum contig (Table 2). Thus, our EST project yielded an approximately equiva- lent number of contigs for A. mexicanum and A. t. tigrinum, and overall we identified > 21,000 different contigs. Assuming that 20% of the contigs correspond to redun- dant loci, which has been found generally in large EST projects [21], we identified transcripts for approximately 17,000 different ambystomatid loci. If ambystomatid sal- amanders have approximately the same number of loci as other vertebrates (e.g. [22]), we have isolated roughly half the expected number of genes in the genome. Ambystoma mexicanum 11190 putative transcripts Ambystoma t. tigrinum 9901 putative transcripts 5619 460 204 5571 5111 4907 NCBI Human RefSeq BLASTX NCBI nr BLASTX Unigene X. tropicalus and X. laevis ESTS TBLASTX No Match 4928 4506 4356 4973 422 150 RFiegfsSuelrtqes, on1fr,BaLnAdSXTeXnoapnudsTUBnLiAgeSnTeXdasetaabracsheess to identify best BLAST hits for Ambystoma contigs searched against NCBI human Results of BLASTX and TBLASTX searches to identify best BLAST hits for Ambystoma contigs searched against NCBI human RefSeq, nr, and Xenopus Unigene databases. Page 3 of 17 (page number not for citation purposes)