Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%), with low degrees of pairwise haplotype divergence within populations (0–1%). COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I ( COI) has been proposed as universal marker for this purpose among animals.
Moura GR, Paredes JA, Santos MA (2010) Development of the genetic code: Insights from a fungal codon reassignment.Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. Moura GR, Paredes JA, Santos MA (2010) Development of the genetic code: Insights from a fungal codon reassignment. Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1985) Nomenclature for incompletely specified bases in nucleic acid sequences. New York: Cold Spring Harbor Laboratory Press Sambrook J, Russell DW (2000) Molecular cloning: a laboratory manual. University of California Santa Cruz Genome Bioinformatics (2010) UCSC Genome Browser. National Library of Medicine (2010) Nucleotide home. EMBL, EBI, Wellcome Trust Sanger Institute (2010) Ensembl release 59. Marshall OJ (2005) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Notredame C, Higgins D, Heringa J (200) T-Coffee: a novel algorithm for multiple sequence alignment. Do CB, Mahabhashyam MS, Brudno M et al (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. 
Edgar R (2004) MUSCLE: Multiple sequence alignment with high score accuracy and high throughput. Katoh K, Misawa K, Kuma K et al (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Subramanian A, Kaufmann M, Morgenstern B (2008) DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Molecular Biology and Evolution 27:221–224 
Gouy M, Guindon S, Gascuel O (2010) SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. #PRIMERS IN BIOEDIT WINDOWS#
Hall T (2005) BioEdit Sequence Alignment Editor for Windows 95/98/NT/XP.
0 kommentar(er)
