BMC Genomics 2004, 5:54 Table 5: Functional annotation of contigs Molecular Function (0016209) antioxidant (0016209) binding (0005488) chaparone (0003754) enzyme regulation (003023) motor (0003774) signal transduction (0004871) structural protein (0005198) transcriptional reg. (0030528) translational reg. (0045182) bone remodeling (0046849) circulation (0008015) immune response (000695) respiratory ex. (0009605) respiratory in. (0009719) stress (0006950) Biological Process (0008150) Cellular (0009987) activation (0001775) aging and death (0008219) communication (0007154) differentiation (0030154) extracellular mat. (0043062) growth and main. (0008151) migration (0016477) motility (0006928) Developmental (0007275) aging (0007568) embryonic (0009790) growth (0040007) morphogenesis (0009653) pigment (0048066) post embryonic (0009791) reproduction (0000003) Physiological (0007582) coagulation (0050817) death and aging (0016265) homeostasis (0042592) metabolism (0008152) secretion (0046903) sex differentiation (0007548) A. mex A. t. tig 25 3117 100 193 73 344 501 296 94 8 23 182 254 72 263 4 158 701 31 4 1731 8 163 32 6 2 350 13 8 42 22 159 22 3059 9 3 29 2578 85 223 75 375 411 221 59 8 78 263 288 58 320 6 148 696 20 4 1445 14 154 21 1 2 272 26 13 27 73 148 27 2513 16 2 Numbers in parentheses reference GO numbers [23]. and protein properties of embryonic stem cells [28], how- ever no new neurons have been observed to derive from these cells in vivo after SCI [29]. Thus, although endogenous neural progenitors of the ependymal layer may have latent regenerative potential in adult mammals, this potential is not realized. Several recently completed microarray analy- ses of spinal cord injury in rat now make it possible to cross-reference information between amphibians and mammals. For example, we searched the complete list of significantly up and down regulated genes from Carmel et http://www.biomedcentral.com/1471-2164/5/54 al. [30] and Song et al. [31] against all Ambystoma ESTs. Based upon amino acid sequence similarity of translated ESTs (TBLASTX; E<10-7), we identified DNA sequences cor- responding to 69 of these 164 SCI rat genes (Table 6). It is likely that we have sequence corresponding to other pre- sumptive orthologues from this list as many of our ESTs only contain a portion of the coding sequence or the untranslated regions (UTR), and in many cases our searches identified closely related gene family members. Thus, many of the genes that show interesting expression patterns after SCI in rat can now be examined in salamander. Similar gene expression programs may underlie regenera- tion of vertebrate appendages such as fish fins and tetrapod limbs. Regeneration could depend on reiterative expression of genes that function in patterning, morphogenesis, and metabolism during normal development and homeostasis. Or, regeneration could depend in part on novel genes that function exclusively in this process. We investigated these alternatives by searching A. mexicanum limb regeneration ESTs against UNIGENE zebrafish fin regeneration ESTs (Figure 3). This search identified 1357 significant BLAST hits (TBLASTX; E<10-7) that corresponded to 1058 unique zebrafish ESTs. We then asked whether any of these poten- tial regeneration homologues were represented uniquely in limb and fin regeneration databases (and not in databases derived from other zebrafish tissues). A search of the 1058 zebrafish ESTs against > 400,000 zebrafish ESTs that were sampled from non-regenerating tissues revealed 43 that were unique to the zebrafish regeneration database (Table 7). Conceivably, these 43 ESTs may represent transcripts important to appendage regeneration. For example, our search identified several genes (e.g. hspc128, pre-B-cell col- ony enhancing factor 1, galectin 4, galectin 8) that may be expressed in progenitor cells that proliferate and differenti- ate during appendage regeneration. Overall, our results sug- gest that regeneration is achieved largely through the reiterative expression of genes having additional functions in other developmental contexts, however a small number of genes may be expressed uniquely during appendage regeneration. DNA sequence polymorphisms within and between A. mexicanum and A. t. tigrinum The identification of single nucleotide polymorphisms (SNPs) within and between orthologous sequences of A. mexicanum and A. t. tigrinum is needed to develop DNA markers for genome mapping [32], quantitative genetic analysis [33], and population genetics [34]. We estimated within species polymorphism for both species by calculat- ing the frequency of SNPs among ESTs within the 20 larg- est contigs (Table 4). These analyses considered a total of 30,638 base positions for A. mexicanum and 18,765 base positions for A. t. tigrinum. Two classes of polymorphism were considered in this analysis: those occurring at Page 6 of 17 (page number not for citation purposes)