title: Genic regions of a large salamander genome contain long introns and novel genes.
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!
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA. smithjj@u.washington.edu
authors.forename: Jeramiah J
authors.initials: JJ
authors.lastname: Smith
authors.forename: Srikrishna
authors.initials: S
authors.lastname: Putta
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Pao
authors.forename: Inder M
authors.initials: IM
authors.lastname: Verma
authors.forename: Tony
authors.initials: T
authors.lastname: Hunter
authors.forename: Susan V
authors.initials: SV
authors.lastname: Bryant
authors.forename: David M
authors.initials: DM
authors.lastname: Gardiner
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Harkins
authors.forename: S Randal
authors.initials: SR
authors.lastname: Voss
mesh_terms: D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D005091:Exons; D020224:Expressed Sequence Tags; D016678:Genome; D006801:Humans; D007438:Introns / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry; D009690:Nucleic Acid Conformation; D014562:Caudata / Q000235:genetics*
chemical_list: D035683:MicroRNAs