Are “universal” DNA primers really universal?

“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I ( COI ) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment o...

Full description

Saved in:
Bibliographic Details
Published in:Journal of applied genetics 2014-11, Vol.55 (4), p.485-496
Main Authors: Sharma, Pranay, Kobayashi, Tsuyoshi
Format: Article
Language:English
Subjects:
Analysis
Animal Genetics and Genomics
Animal Genetics • Original Paper
Animalia
Biomedical and Life Sciences
Cytochrome oxidase
DNA
Human Genetics
Life Sciences
Marine
Microbial Genetics and Genomics
Plant Genetics and Genomics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I ( COI ) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the COI gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725 COI sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725 COI primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA), F 6,188  = 8.193, P  
ISSN:1234-1983
2190-3883
DOI:10.1007/s13353-014-0218-9