A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta)

Our previous study of the North American biogeography of Bangia revealed th e presence of two introns inserted at positions 516 and 1506 in the nuclear -encoded SSU rRNA gene. We subsequently sequenced nuclear SSU rRNA in addit ional representatives of this genus and the sister genus Porphyra in order to examine the distribution, phylogeny, and structural characteristics of t hese group I introns. The lengths of these introns varied considerably, ran ging from 467 to 997 nt for intron 516 and from 509 to 1,082 nt for intron 1506. The larger introns contained large insertions in the P2 domain of int ron 516 and the P1 domain of intron 1506 that correspond to open reading fr ames (ORFs) with His-Cys box homing endonuclease motifs. These ORFs were fo und on the complementary strand of the 1506 intron in Porphyra fucicola and P. umbilicalis (HG), unlike the 516 intron in P. abbottae, P. kanakaensis, P. tenera (SK), Bangia fuscopurpurea (Helgoland), and B. fuscopurpurea (MA ). Frameshifts were noted in the ORFs of the 516 introns in P. kanakaensis and B. fuscopurpurea (HL), and all ORFs terminated prematurely relative to the amino acid sequence for the homing endonuclease I-Ppo 1. This raises th e possibility that these sequences are pseudogenes. Phylogenies generated u sing sequences of both introns and the 18S rRNA gene were congruent, which indicated long-term immobility and vertical inheritance of the introns foll owed by subsequent loss in more derived lineages. The introns within the fl orideophyte species Hildenbrandia rubra (position 1506) were included to de termine relationships with those in the Bangiales. The two sequences of int ron 1506 analyzed in Hildenbrandia were positioned on a well-supported bran ch associated with members of the Bangiales, indicating possible common anc estry. Structural analysis of the intron sequences revealed a signature str uctural feature in the P5b domain of intron 516 that is unique to all Bangi alean introns in this position and not seen in intron 1506 or other group I CI introns.