Genic Regions of a Large Salamander Genome Contain Long Introns and Novel Genes

Authors

Jeramiah J. Smith, University of KentuckyFollow
Srikrishna Putta, University of KentuckyFollow
Wei Zhu, The Salk Institute for Biological Studies
Gerald M. Pao, The Salk Institute for Biological Studies
Inder M. Verma, The Salk Institute for Biological Studies
Tony Hunter, The Salk Institute for Biological Studies
Susan V. Bryant, University of California, Irvine
David M. Gardiner, University of California, Irvine
Timothy T. Harkins, Roche Applied Science
S. Randal Voss, University of KentuckyFollow

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 x 10(9) 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 10x 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 5x 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.

Document Type

Article

Publication Date

1-13-2009

Notes/Citation Information

Published in BMC Genomics, v. 10, 19.

© 2009 Smith et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Digital Object Identifier (DOI)

http://dx.doi.org/10.1186/1471-2164-10-19

Repository Citation

Smith, Jeramiah J.; Putta, Srikrishna; Zhu, Wei; Pao, Gerald M.; Verma, Inder M.; Hunter, Tony; Bryant, Susan V.; Gardiner, David M.; Harkins, Timothy T.; and Voss, S. Randal, "Genic Regions of a Large Salamander Genome Contain Long Introns and Novel Genes" (2009). Biology Faculty Publications. 8.
https://uknowledge.uky.edu/biology_facpub/8