Group I introns, which are widespread in nature, carry out RNA self-splicing. The secondary structure common to these introns was for the most part established a decade ago. Information about their higher order structure has been derived from a range of experimental approaches, comparative sequence analysis, and molecular modelling. This information now provides the basis for a new two-dimensional structural diagram that more accurately represents the domain organization and orientation of helices within the intron, the coaxial stacking of certain helices, and the proximity of key nucleotides in three-dimensional space. It is hoped that this format will facilitate the detailed comparison of group I intron structures.

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We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.

Group I introns are widespread in eukaryotic organelles and nuclear-encoded ribosomal DNAs (rDNAs). The green algae are particularly rich in rDNA group I introns. To better understand the origins and phylogenetic relationships of green algal nuclear-encoded small subunit rDNA group I introns, a secondary structure-based alignment was constructed with available intron sequences and 11 new subgroup ICI and three new subgroup IB3 intron sequences determined from members of the Trebouxiophyceae (common phycobiont components of lichen) and the Ulvophyceae. Phylogenetic analyses using a weighted maximum-parsimony method showed that most group I introns form distinct lineages defined by insertion sites within the SSU rDNA. The comparison of topologies defining the phylogenetic relationships of 12 members of the 1512 group I intron insertion site lineage (position relative to the E. coli SSU rDNA coding region) with that of the host cells (i.e., SSU rDNAs) that contain these introns provided insights into the possible origin, stability, loss, and lateral transfer of ICI group I introns. The phylogenetic data were consistent with a viral origin of the 1512 group I intron in the green algae. This intron appears to have originated, minimally, within the SSU rDNA of the common ancestor of the trebouxiophytes and has subsequently been vertically inherited within this algal lineage with loss of the intron in some taxa. The phylogenetic analyses also suggested that the 1512 intron was laterally transferred among later-diverging trebouxiophytes; these algal taxa may have coexisted in a developing lichen thallus, thus facilitating cell-to-cell contact and the lateral transfer. Comparison of available group I intron sequences from the nuclear-encoded SSU rDNA of phycobiont and mycobiont components of lichens demonstrated that these sequences have independent origins and are not the result of lateral transfer from one component to the other.

Group I introns are found in organellar genomes, in the genomes of eubacteria and phages, and in nuclear-encoded rRNAs. The origin and distribution of nuclear-encoded rRNA group I introns are not understood. To elucidate their evolutionary relationships, we analyzed diverse nuclear-encoded small-subunit rRNA group I introns icluding nine sequences from the green-algal order Zygnematales (Charophyceae). Phylogenetic analyses of group I introns and rRNA coding regions suggest that lateral transfers have occurred in the evolutionary history of group I introns and that, after transfer, some of these elements may form stable components of the host-cell nuclear genomes. The Zygnematales introns, which share a common insertion site (position 1506 relative to the Escherchia cofi small-subunit rRNA), form one subfamily o group I introns that has, after its origin, been inherited through common ancestry. Since the first Zygnematales appear in the middle Devonian within the fossil record, the "1506" group I intron presumably has been a stable component of the Zygnematales small-subunit rRNA coding region for 350-400 million years.Group I introns are characterized by conserved RNA secondary structures essential for splicing and are often capable of self-splicing or require protein factors for excision (1-3). The origin and distribution of group I introns are not understood. Group I introns have been found most often in the organellar and nuclear genomes ofgreen algae, higher plants, and fungi and in the genomes of some eubacteria and phages (3). Since the phage group I introns are readily mobile and the phage genome represents a mosaic of gene segments, it is not possible to address group I intron origin with these sequences (4). Of the organellar group I introns, some contain an open reading frame (ORF) which encodes a sequence-specific endonuclease to mediate their lateral transfer into homologous sequences [intron homing (5)]. Group I intron mobility is also postulated to result from reverse splicing (6).Some group I introns which lack endonuclease coding regions appear to be nonmobile and provide a potentially valuable tool for tracing the evolutionary history of these sequences (2): the presence of a nonmobile group I intron positioned in thq homologous site of the tRNALeu of cyanobacteria and in plastids of photosynthetic lineages that diverged as representatives of the eukaryotic crown group (7, 8) radiation (e.g., green algae, land plants, heterokonts, glaucocystophytes) suggests that this intron was present in the progenitor(s) of these plastids and therefore is at least one billion years old (9). Within eukaryotes, the apparent absence of group I introns within the earliest-diverging amitochondrial and aplastidial Archezoa (see ref. 10 for definition) suggests that they were introduced into the nucleus of later-diverging species (i.e., Metakaryota) by gene transfer from the intron-containing cyanobacterium that gave rise to the plastid [i.e., tRNA'-eu group I intron (4, 9)] or the a purple eubacterium that...