{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T04:41:00Z","timestamp":1745469660181,"version":"3.40.4"},"reference-count":89,"publisher":"S. Karger AG","issue":"2-4","license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.karger.com\/Services\/SiteLicenses"},{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.karger.com\/Services\/SiteLicenses"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cytogenet Genome Res"],"published-print":{"date-parts":[[2009]]},"abstract":"<jats:p>Genome projects have revolutionized our understanding of both molecular biology and evolution, but there has been a limited collection of genomic data from reptiles. This is surprising given the pivotal position of reptiles in vertebrate phylogeny and the potential utility of information from reptiles for understanding a number of biological phenomena, such as sex determination. Although there are many potential uses for genomic data, one important and useful approach is phylogenomics. Here we report cDNA sequences for the c-&lt;i&gt;Jun&lt;\/i&gt;&lt;i&gt;(JUN) &lt;\/i&gt;and &lt;i&gt;DJ-1&lt;\/i&gt;&lt;i&gt;(PARK7)&lt;\/i&gt; proto-oncogenes from 3 reptiles (the American alligator, Nile crocodile, and Florida red-belly turtle), show that both genes are expressed in the alligator, and integrate them into analyses of their homologs from other organisms. With these taxa it was possible to conduct analyses that include all major vertebrate lineages. Analyses of c-&lt;i&gt;Jun&lt;\/i&gt; revealed an unexpected but well-supported frog-turtle clade while analyses of&lt;i&gt; DJ-1&lt;\/i&gt; revealed a topology largely congruent with expectation based upon other data. The conflict between the c-&lt;i&gt;Jun&lt;\/i&gt; topology and expectation appears to reflect the overlap between c-&lt;i&gt;Jun&lt;\/i&gt; and a CpG island in most taxa, including crocodilians. This CpG island is absent in the frog and turtle, and convergence in base composition appears to be at least partially responsible for the signal uniting these taxa. Noise reduction approaches can eliminate the unexpected frog-turtle clade, demonstrating that multiple signals are present in the c-&lt;i&gt;Jun&lt;\/i&gt; alignment. We used phylogenetic methods to visualize these signals; we suggest that examining both historical and non-historical signals will prove important for phylogenomic analyses.<\/jats:p>","DOI":"10.1159\/000297715","type":"journal-article","created":{"date-parts":[[2010,4,28]],"date-time":"2010-04-28T06:58:23Z","timestamp":1272437903000},"page":"79-93","source":"Crossref","is-referenced-by-count":15,"title":["From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-&lt;i&gt;Jun&lt;\/i&gt; and &lt;i&gt;DJ-1&lt;\/i&gt; Proto-Oncogenes"],"prefix":"10.1159","volume":"127","author":[{"given":"Y.","family":"Katsu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.L.","family":"Braun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L.J.","family":"Guillette, 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