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

Jeramiah J. Smith, Srikrishna Putta, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony Hunter, Susan V. Bryant, David M. Gardiner, Timothy T. Harkins, S. Randal Randal

Research output: Contribution to journalArticlepeer-review

71 Scopus citations


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.

Original languageEnglish
Article number19
JournalBMC Genomics
StatePublished - Jan 13 2009

Bibliographical note

Funding Information:
This project was supported by grants R24-RR016344 and P20-RR016741 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCRR or NIH. The project was also supported by a Roche genome sequencing award and funding from the California Institute for Regenerative Medicine, University of Kentucky College of Arts and Sciences and Biology Department, and Kentucky Bioinformatics Research Infrastructure Network. The Spinal Cord and Brain Injury Research Center and the National Science Foundation supported Ambystoma Genetic Stock Center (DBI-0443496) provided resources and facilities.

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


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