Ambystoma LG1 V2_p2_g6 V2_p2_h2 V2_p3_a5 V2_p3_b1 V2_p5_b3 V2_p5_h3 V2_p6_a4 V3_p1_a21 V3_p1_b13 0.0 cM DLX3 HSPC009 SUI1 KRT10 KRT17 FLJ13855 HOXB13 RPL19 THRα 63.7 cM gFCrioogmuuprpea1r4iasnodn aonf 1ge1nMeborrdeegriobneotwfHeesna1A7m(b3y7s.t7omMablitnok4ag8e.7 Mb) Comparison of gene order between Ambystoma link- age group 1 and an 11 Mb region of Hsa17 (37.7 Mb to 48.7 Mb). Lines connect the positions of putatively orthologous genes. Comparative gene mapping Salamanders occupy a pivotal phylogenetic position for reconstructing the ancestral tetrapod genome structure and for providing perspective on the extremely derived anuran Xenopus (37) that is currently providing the bulk of amphibian genome information. Here we show the BMC Genomics 2004, 5:54 http://www.biomedcentral.com/1471-2164/5/54 Table 8: EST loci used in a population-level PCR amplification screen in A. ordinarium (Continued) AGAATTCCCAATAGCACCTGAAAT CTTTTTGGCCTGGTCTTTTTG TTTACACAGAAACCTTGTTTATTTGGC AGTCACTGTGTTACATTATCACCCAC AATGGGATGAAGAGCGAGAAT CCTTCAGACGAAAACAGCACTAAG AGAAATACATCAAATATCGGGTGG ACCAAGTTCTTGGAAAGTGGTG GTCTTGGTACTCAATGAAGGAGATG CACTTGGTAAATACATACACACAGCA AGATTCTTCAGACTCGTCCTTCTTT TTTAAGGATGCTTAGAGGCAAAGTATT TATACACTGCGGTCTGCATCTACT CTGCCCCATTGACATTTACCTA TACAGTGTATGAGAGCCCAATATTTC AAAAAGGACAATGTTCAGCTCTCT CTTAGTGTCTCCTGGGTTTGAATAG TCAATCTGATGAAGAGTTTACATGTCT HSA 17 48736 Kb 48544 47460 47279 41323 40149 40218 39348 38596 37732 Kb utility of ambystomatid ESTs for identifying chromo- somal regions that are conserved between salamanders and other vertebrates. A region of conserved synteny that corresponds to human chromosome (Hsa) 17q has been identified in several non-mammalian taxa including rep- tiles (38) and fishes (39). In a previous study Voss et al. (40) identified a region of conserved synteny between Ambystoma and Hsa 17q that included collagen type 1 alpha 1 (Col1a1), thyroid hormone receptor alpha (Thra), homeo box b13 (Hoxb13), and distal-less 3 (Dlx3) (Figure 4). To evaluate both the technical feasibility of mapping ESTs and the likelihood that presumptive orthologues map to the same synteny group, we searched our assem- blies for presumptive Hsa 17 orthologues and then developed a subset of these loci for genetic linkage map- ping. Using a joint assembly of A. mexicanum and A. t. tigrinum contigs, 97 Hsa 17 presumptive orthologues were identified. We chose 15 genes from this list and designed PCR primers to amplify a short DNA fragment containing 1 or more presumptive SNPs that were identified in the joint assembly (Table 9). All but two of these genes were mapped, indicating a high probability of mapping success using markers developed from the joint assembly of A. mexicanum and A. t. tigrinum contigs. All 6 ESTs that exhibited 'best hits' to loci within the previously defined human-Ambystoma synteny group did map to this region (Hspc009, Sui1, Krt17, Krt24, Flj13855, and Rpl19). Our results show that BLAST-based definitions of orthology are informative between salamanders and human. All other presumptive Hsa 17 loci mapped to Ambystoma chromosomal regions outside of the previously defined synteny group. It is interesting to note that two of these loci mapped to the same ambystomatid linkage group (Cgi-125, Flj20345), but in human the presumptive ortho- logues are 50 Mb apart and distantly flank the syntenic loci in Figure 4. Assuming orthology has been assigned correctly for these loci, this suggests a dynamic history for some Hsa 17 orthologues during vertebrate evolution. Future directions Ambystomatid salamanders are classic model organisms that continue to inform biological research in a variety of areas. Their future importance in regenerative biology and Page 13 of 17 (page number not for citation purposes)