Among 2212 intron positions in regions of good alignment, we found only 27 species-specific introns, 19 in P. We studied orthologous gene pairs from the human malaria parasite Plasmodium falciparum and the rodent parasite Plasmodium yoelii, which diverged ≥100 million years ago (Mya). 2003 Roy and Gilbert 2005b, 2006) or the diversity of intron-rich parasites and species with large population sizes. Traditional selection-based explanations ( Doolittle and Sapienza 1980 Gilbert 1987 Lynch 2002) do not predict recent findings of intron-rich early eukaryotes ( Fedorov et al. 2002), and often even within eukaryotic groups. Intron number varies massively across eukaryotes, from hundreds of thousands of introns per vertebrate genome to only two characterized introns in Giardia lamblia ( Venter et al. 2005 Roy and Gilbert 2005a) or by simple genomic deletion of the intron sequence ( Robertson 1998 Kent and Zahler 2000 Banyai and Patthy 2004 Cho et al. 2003 Mourier and Jeffares 2003 Sverdlov et al. 1986 Fink 1987 Long and Langley 1993 Derr 1998 Sakurai et al. Intron loss might occur by recombination with a reverse-transcribed copy of a spliced mRNA transcript ( Perler et al. 1998, 19), or (3) reinsertion of a spliced RNA copy of an intron into a previously intron-less site of a transcript, followed by reverse transcription of this transcript and gene conversion ( Cavalier-Smith 1985 Palmer and Logsdon Jr. New introns might arise either by (1) insertion of type II self-splicing introns laterally transferred from endosymbionts ( Sharp 1985 Cavalier-Smith 1991 Stoltzfus 1999), (2) insertion of transposable elements into coding sequences ( Crick 1979 Iwamoto et al. The mechanisms of intron loss and gain also remain debated. 2005), with a more central role for intron gain ( Babenko et al. However, other analyses suggest more moderate ancestral intron densities ( Csuros 2005 Nguyen et al. This view is supported by the apparent presence of a complex spliceosome in the eukaryotic ancestor ( Collins and Penny 2005) and by the two available genome-wide studies of more closely related species ( Roy et al. 2005) in a pattern suggesting intron-rich ancestors and massive recurrent intron loss along diverse lineages ( Roy and Gilbert 2005b). Introns are often found at the exact same positions in orthologous genes of widely divergent eukaryotic species ( Fedorov et al. 2006 Roy and Gilbert 2006).Ī central issue is the relative importance of intron loss and gain through eukaryotic history. The ultimate origins and evolutionary significance of spliceosomal introns have been hotly debated since their discovery 30 years ago (for recent reviews, see Rogozin et al. They are excised from mRNA transcripts by the spliceosome, an elaborate RNA–protein complex. Spliceosomal introns are largely quasi-random sequences that interrupt the coding regions of many eukaryotic genes. The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number. ![]() ![]() The dearth of intron loss and gain could be explained by the lack of known transposable elements in Plasmodium, since transposable elements and/or reverse transcriptase are thought to be necessary for both processes. Two changes occurred in the chloroquine resistance transporter, suggesting a role for positive selection in intron loss in Plasmodium. ![]() Many of the intron changes occurred in genes encoding proteins involved in nucleic acid-related processes, as previously found for intron gains in nematodes. ![]() That all observed changes were exact, occurring without loss or gain of flanking coding sequence, suggests intron loss via an mRNA intermediate, as does a nonsignificant trend toward loss of introns at adjacent positions. The implied intron loss and gain rates are much lower than previously estimated for nematodes, arthropods, fungi, and plants, and are comparable only with the rates in vertebrates. Intron presence in related species shows that at least 19 and possibly 26 of the changes are due to intron loss, depending on phylogeny. Only 27 out of 2212 positions were specific to one of the two species. We compared intron positions in conserved regions of 3479 orthologous gene pairs from Plasmodium falciparum and Plasmodium yoelii, which likely diverged ≥100 million years ago (Mya).
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |