Comparison of RAPD, STS, ISSR and AFLP molecular methods used for assessment of genetic diversity in hop (Humulus lupulus L.) |
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| Authors: | Josef Patzak |
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| Institution: | 1. Hop Research Institute Co. Ltd., Kadaňská 2525, ?atec, 438 46, Czech Republic
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| Abstract: | CoxI genomic and cDNA sequences from gymnosperms and angiosperms were used to study the effects of RNA editing on gene evolution
and phylogenyre construction. In six gymnosperms harboring edited coxI gene the number of nucleotide substitutions at 1st, 2nd and 3rd codon positions was similar. In contrast, in angiosperms, the number of nucleotide substitutions at 1st and 2nd codon positions was much lower than at the 3rd. The coxI gene in long-lived gymnosperms evolved much faster than in annual angiosperms. This accelerated rate of nucleotide substitution
in gymnosperms is due to accumulation of T-C substitutions at edited sites that can randomly appear at all three codon positions.
Editing predominantly occurred at 1st and 2nd codon positions as a result of selection against non synonymous T-C substitutions and other types of mutations. The tree
topologies for the investigated species based on genomic DNA data were in concordance with their taxonomic positions. The
trees based on polymorphic edited sites agreed with trees derived from complete sequence information. This indicates that
edited sites are reliable sources of phylogenetic information especially for species that contain many edited sites. However,
the fast evolution rate of coxI gene in gymnosperms has caused the long branches in the phylogenetic trees. The inclusion of the species with a processed
paralog i.e., edited form of the coxI gene, affected the topology of phylogenetic trees, especially when the taxon with a processed paralog was closely related
to the other species analyzed.
This revised version was published online in July 2006 with corrections to the Cover Date. |
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| Keywords: | coxI evolution gymnosperms phylogeny RNA editing |
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