Research article

Genic regions of a large salamander genome contain long introns and novel genes

Jeramiah J Smith^1,6,7 , Srikrishna Putta¹ , Wei Zhu² , Gerald M Pao² , Inder M Verma² , Tony Hunter² , Susan V Bryant^3,4 , David M Gardiner^3,4 , Timothy T Harkins⁵ and S Randal Voss¹

¹Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA

²The Salk Institute for Biological Studies, La Jolla, CA 92037, USA

³Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA

⁴The Developmental Biology Center, University of California Irvine, Irvine, CA 92697, USA

⁵Roche Applied Science, Indianapolis, IN 46250, USA

⁶University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA

⁷Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA

author email corresponding author email

BMC Genomics 2009, 10:19doi:10.1186/1471-2164-10-19

Published:	13 January 2009

Abstract

Background

The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 10⁹ bp) were isolated and sequenced to characterize the structure of genic regions.

Results

Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86%) of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases!

Conclusion

This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.