Data from: Rapid identification of chloroplast haplotypes using High-Resolution Melting analysis ...
We have evaluated High Resolution Melt (HRM) analysis as a method for one-step haplotype identification in phylogeographic analysis. Using two adjoined internal amplicons (c.360 and 390bp) at the chloroplast rps16 intron (c.750bp) we applied HRM to identify haplotypes in 21 populations of two Europe...
| Main Authors: | , , , |
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| Format: | Dataset |
| Language: | English |
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Dryad
2012
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.s904k https://datadryad.org/stash/dataset/doi:10.5061/dryad.s904k |
| Summary: | We have evaluated High Resolution Melt (HRM) analysis as a method for one-step haplotype identification in phylogeographic analysis. Using two adjoined internal amplicons (c.360 and 390bp) at the chloroplast rps16 intron (c.750bp) we applied HRM to identify haplotypes in 21 populations of two European arctic-alpine herb species Arenaria ciliata and A. norvegica (Caryophyllaceae). From 446 accessions studied, 20 composite rps16 haplotypes were identified by the melt-curve protocol, 18 of which could be identified uniquely. In a comparative sensitivity analysis with in silico PCR-RFLP, only 7 of these 20 haplotypes could be identified uniquely. Observed in vitro experimental HRM profiles were corroborated by in silico HRM analysis generated on uMeltSM. In silico mutation analysis carried out on a 360bp wild-type rps16I amplicon determined that the expected rate of missed SNP detection in vitro was similar to existing evaluations of HRM sensitivity, with transversion SNPs being more likely to go undetected ... : Dang et al HRM Aligned rps16 sequencesAligned rps16 sequences for 20 haplotypes of Arenaria ciliata and A. norvegica (C01-c18, and N01-N02 resepctively). Alignment presented in fasta format and saved as .txt. ... |
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