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Background  Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus  Porphyra  (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different  Porphyra spiralis  var.  amplifolia  ( PSA ) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these  PSA  populations, in addition to  cox 2-3 and  rbc L-S regions. Introns of different sizes were tested qualitatively for  in vitro  self-splicing.    Results  Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of  PSA  in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of  PSA , these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five  cox 2-3 haplotypes and the unique  rbc L-S haplotype were used as markers for summary statistics, neutrality tests Tajima's  D  and Fu's  Fs  and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for  PSA  populations with the three analyses.  In vitro  experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts.    Conclusion  The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for  PSA  populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of  Porphyra;  and intron size polymorphism as a marker for population genetics.

bmc evolutionary biology

Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America