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

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

doi:10.1186/1471-2164-10-19

Abstract

BackgroundThe 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.ResultsAnnotation 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!ConclusionThis 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.

Highlights

The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes
The sequence coverage provided by the assemblies approximated the estimated size of bacterial artificial chromosome (BAC) clones on agarose gels
Very few repetitive DNA sequences were identified overall within axolotl BACs, with retrotransposons representing the largest fraction (Table 3). These results suggest that genic regions of the axolotl are not completely structured by repetitive sequences

Summary

Introduction

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. It was established before the advent of DNA sequencing that organisms show incredible variation in genome size. The paradox was partially resolved by partitioning overall genome size into two compartments: protein coding vs non-protein coding This partition showed that organisms tend to have similar numbers of genes but non-coding and presumptively non-functional portions of genomes vary greatly [2]. The amount of non-coding DNA does scale with developmental complexity in some comparative studies [18] These findings are motivating renewed interest into genome diversity and function. DNA sequence data are completely lacking for organisms with large genomes

Methods

Results

Discussion

Conclusion