title: SNPs and Hox gene mapping in Ciona intestinalis.
abstract: BACKGROUND
  The tunicate Ciona intestinalis (Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of C. intestinalis SNP (Single Nucleotide Polymorphism) markers. A SNP subset was used to determine the genetic distance between Hox-5 and -10 genes.
  
  
  RESULTS
  DNA fragments were amplified from 12 regions of C. intestinalis sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the Hox5 and Hox10 intragenic regions. In C. intestinalis, these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5. A subset of the above primers was used to perform successful amplification in C. intestinalis sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the Hox-5 and -10 loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function). Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation.
  
  
  CONCLUSIONS
  SNPs here described allow analysis and comparisons within and between C. intestinalis cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.
authors.affiliation: Department of Biochemistry and Molecular Biology, Stazione Zoologica A. Dohrn, Napoli, Villa Comunale, Italy. caputi@szn.it
authors.forename: Luigi
authors.initials: L
authors.lastname: Caputi
authors.forename: Marco
authors.initials: M
authors.lastname: Borra
authors.forename: Nikos
authors.initials: N
authors.lastname: Andreakis
authors.forename: Elio
authors.initials: E
authors.lastname: Biffali
authors.forename: Paolo
authors.initials: P
authors.lastname: Sordino
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D002938:Ciona intestinalis / Q000145:classification / Q000235:genetics*; D004247:DNA / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D005091:Exons; D005801:Genes, Homeobox; D006239:Haplotypes; D007438:Introns; D015810:Linkage Disequilibrium; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004247:DNA