MBE Advance Access originally published online on May 23, 2007
Molecular Biology and Evolution 2007 24(9):1926-1933; doi:10.1093/molbev/msm102
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Research Articles |
Widespread Intron Loss Suggests Retrotransposon Activity in Ancient Apicomplexans
* Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
E-mail: scottwroy{at}gmail.com.
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Abstract |
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Several facets of spliceosomal intron in apicomplexans remain mysterious. First, intron numbers vary across species by 2 orders of magnitude, indicating massive intron loss and/or gain. Second, previous studies have shown very different evolutionary patterns over different timescales, with 100-fold higher rates of intron loss/gain between genera than within genera. Third, the timing and dynamics of nearly complete intron loss in Cryptosporidium species, as well as reasons for retention of the few remaining introns, remain unknown. We compared intron positions in 785 orthologous genes between 3 moderate to intron-rich apicomplexan species. We estimate that the Theileria-Plasmodium ancestor had 4.5 times as many introns as modern Plasmodium species and 38% more than modern Theileria species, and that subsequent intron losses have outnumbered intron gains by 5.8 to 1 in Theileria and by some 56 to 1 in Plasmodium. Several patterns suggest that these intron losses occurred by recombination with reverse-transcribed mRNAs. Intriguingly, this finding suggests significant retrotransposon activity in the lineages leading to both Theileria and Plasmodium, in contrast to the dearth of known retrotransposons and intron loss within modern species from both genera. We also compared genomes from Cryptosporidium parvum and C. hominis and found no evidence of ongoing intron loss, nor of intron gain. By contrast, Cryptosporidium introns are less evolutionary conserved with Toxoplasma than are introns from other apicomplexans; thus the few remaining introns are not simply indispensable ancestral introns.
Key Words: intron loss • intron gain • genome evolution • retrotransposon evolution • selfish DNA
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Introduction |
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Large-scale sequencing of a broad diversity of eukaryotic species has revealed pronounced differences in a variety of features: genome size, gene number, activity and number of transposable elements, degree of alternative splicing, and the density and lengths of spliceosomal introns. The increasingly broad phylogenetic sampling of sequenced species has also revealed the lack of a simple relationship between these various aspects of genome organization. While some species' genomes seem quite generally "simple" (Encephalitozoon cuniculi has a compact genome with few genes and very few short introns; Katinka et al. 2001
) or "complex" (Homo sapiens has a 3-Gb genome, over 20,000 genes, more than 8 introns per gene on average, extensive alternative splicing, and abundant transposable element derived sequence; Lander et al. 2001), other species defy such clear characterization. For instance, the Bigelowiella natans nucleomorph, an enslaved algal nucleus, represents an extreme of genomic compaction in most genomic features but still retains more than 3 introns on average per gene (Gilson and McFadden 1996; Gilson et al. 2006). The genome of Takifugu rubripes contains numerous introns but relatively few transposable elements; the genome of Oryza sativa contains abundant transposable elements but has generally short introns (Aparicio et al. 2002; Yu et al. 2002). The explanations for these patterns remain obscure.
Here we further investigate an example of partial genome compaction in the phylum Apicomplexa. Apicomplexans are single-celled parasites of animals with complex life cycles. The large numbers of introns in most species are perhaps surprising in light of the generally reductive mode of evolution observed in various parasitic lineages (Katinka et al. 2001; Gardner et al. 2002, 2005; Abrahamsen et al. 2004; Sakharkar, Dhar, and Chow 2004). While species of the apicomplexan genus Cryptosporidium have a very small number of introns (only around 5% of genes in the fully sequenced C. parvum genome contain introns; Abrahamsen et al. 2004), in keeping with a variety of other unicellular parasites (Giardia lamblia, Typanosoma sp., Trichomonas vaginalis, Encephalitozoon cuniculi), most characterized apicomplexan lineages exhibit moderate to high intron densities (roughly 1, 2, and 5 introns per gene on average in Plasmodium and Theileria species and in Toxoplasma gondii, respectively; compiled in Jeffares, Mourier, and Penny 2006; Roy and Gilbert 2006).
We previously showed mysterious contrasting patterns of intron evolution in apicomplexans over different timescales. Rates of intron loss/gain are extremely low within genera (less than 1.5% intron loss/gain over 
100 My for both Plasmodium and Theileria), but are 100- to 1,000-fold higher between genera (only one-sixth of intron positions are shared between Plasmodium and Theileria; Roy and Hartl 2006; Roy and Penny 2006). At a deeper evolutionary level only one-third of Plasmodium falciparum intron positions are shared with surveyed nonapicomplexans (Rogozin et al. 2003).
A second evolutionary mystery involves near-complete genome-wide intron loss, a surprisingly common occurrence in diverse eukaryotic lineages. At least roughly one-third of P. falciparum introns are ancestral to apicomplexans (intron positions shared with nonapicomplexans; Rogozin et al. 2003), indicating near-complete intron loss in Cryptosporidium. Analogous cases can be made for each nearly intronless eukaryotic lineage (Rogozin et al. 2003; Slamovits and Keeling 2006). The dynamics of these dramatic reductions are not well understood: first whether loss in these lineages is episodic or ongoing, and second why these species retain their few remaining introns.
We report 2 studies of intron position conservation in apicomplexans. First, we compared orthologous gene trios between P. falciparum, T. parva, and T. gondii. We estimate that the Plasmodium-Theileria ancestor had 4.5 times as many introns as P. falciparum and 38% more introns than T. parva. We further estimate that losses have outnumbered gains by 5.8 to 1 in T. parva, and by a striking 56 to 1 in P. falciparum. Nearly all observed intron losses are exact, occurring without loss/gain of adjacent coding sequences. Intron losses are 3' biased, and loss of introns that are adjacent along the gene is more common than expected by random single loss. These patterns suggest intron loss by recombination with reverse transcribed copies of mRNAs. This in turn suggests significant retrotransposon activity in lineages leading to Plasmodium and Theileria, whereas the dearth of intron loss (and retrotransposons) within those genera suggest more recent, convergent (near) extinction of retrotransposons in both lineages.
Second, we report a genome-wide comparison of introns in Cryptosporidium species. We find no intron loss or gain since the C. parvum-C. hominis divergence (Abrahamsen et al. 2004; Xu et al. 2004). However, over much longer evolutionary timescales, C. parvum intron positions are relatively not highly conserved: only 36.7% of C. parvum intron positions are shared with T. gondii, less than for more intron-rich P. falciparum (71.6%) and T. parva (70.6%). Thus the small subset of introns present in Cryptosporidium species do not simply represent a broadly evolutionary-conserved set of functionally important ancestral introns.
These results indicate that the relatively high intron densities among parasites found in Plasmodium and Theileria species in fact represent reductions from the ancestral genomes of ancestors (which were also parasitic), and that there is no evidence for significant ongoing intron loss in Cryptosporidium. We discuss the implications for the evolutionary forces controlling genome structure.
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Material and Methods |
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We downloaded the annotated genome sequences for T. parva, C. parvum, and C. hominis (Genbank accession numbers AAGK01000001.1, AAEE01000000, and AAEL01000001.1, respectively) and for P. falciparum (http://www.plasmodb.org, version 10.03.2002.v2) and T. gondii (http://www.toxodb.org). Putatively orthologous gene pairs/trios were determined by reciprocal BLASTP searches. Intron positions were mapped onto ClustalW alignments and computationally filtered. Intron positions within 5 codons were considered to be conserved (which applied in less than 3% of cases for the T. gondii-T. parva-P. falciparum alignments). Conserved positions were conservatively defined as 50% conservation in the flanking 10 amino acids between each pair of species, as previously described (Roy and Hartl 2006
). Alignments were further analyzed by eye. The programs used are available from the authors.
Ancestral intron numbers and numbers of subsequent intron losses and gains were estimated using previously described methods (Roy and Gilbert 2005b, c). Given the small number of species, other methods that attempt to account for parallel insertion are not applicable (Csuros 2005; Nguyen et al. 2005; Carmel et al. 2007). Fortunately, parallel gains are very unlikely to be a significant issue in the lineages studied. First, we estimate only 15 gains in Plasmodium and 65 gains in Theileria over 785 genes. Assuming equal rates of insertion across genes, we therefore expect only around 1 gene to have experienced a gain in both lineages (15 x 65 / 785), and even assuming very restricted insertion, the chance that both gained introns would insert into the identical site is very small. Second, using greater taxonomic sampling, Nguyen and coauthors (2007) reached similar conclusions about relative rates of loss and gain in these lineages while attempting to account for parallel intron gain. As such, we are confident that our estimates are not significantly affected by parallel gain.
For the C. parvum-C. hominis comparison, we performed BLASTN searches of coding sequences from intron-containing C. parvum genes against the C. hominis genome, and evaluated intron presence/absence on the presence/absence of an alignment gap. Of the 180 annotated C. parvum introns, 3 were discarded due to implausibly short lengths (<5 bp), and 1 was excluded because proximity to the 5' of the gene made intron presence/absence impossible to ascertain. Orthologous sequence was identified for 164/176 of the remaining introns, all of which showed intron presence.
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Results |
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Intron Loss and Gain in Apicomplexans
To characterize the relative contributions of intron loss and gain in the evolutionary history of Plasmodium and Theileria, we compared intron positions in trios of orthologous genes between relatively intron-poor Plasmodium falciparum, more moderate Theileria parva, and very intron-rich outgroup Toxoplasma gondii. Within highly conserved regions of 785 ortholog trios, there were 249 introns in P. falciparum, 814 in T. parva, and 1,331 in T. gondii. In total, there were 1,604 intron positions. The relationship between apicomplexans with fully sequenced genomes used in this and other studies is given in figure 1.
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Some genes showed very highly conserved intron-exon structures across the species (fig. 2). Others showed several introns that were shared between the outgroup T. gondii and 1 (but not the other) of the other 2 species, suggesting intron loss (fig. 3). In total, 7.4% of intron positions were shared across all 3 species, 34.4% were shared between exactly 2 species (82.6% of these were T. gondii-T. parva introns), and 58.2% were species-specific (74.6% in T. gondii, only 3.6% in intron-poor P. falciparum; fig. 4A).
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We used previously described methods (Nielsen et al. 2004
; Roy and Gilbert 2005b, c) to estimate the number of introns in the analyzed regions for the T. parva-P. falciparum ancestor and the subsequent numbers of intron losses and gains (fig. 4B). The T. parva-P. falciparum ancestor is estimated to have had 1,227 introns in analyzed regions, which is 38% more introns than T. parva and 4.5 times as many introns as P. falciparum. P. falciparum is estimated to have experienced 16 intron gains and 893 intron losses since the Plasmodium-Theileria divergence, or 56 times more losses than gains. T. parva is estimated to have experienced 5.8 times as many losses as gains (378 vs. 65). Of the 753 introns that are species-specific between P. falciparum and T. parva, only around 11% (81/753) are estimated to be due to intron gain. Thus intron loss has been the dominant mode of evolution since the Theileria-Plasmodium divergence.
Evidence for Reverse Transcriptase–Mediated Intron Loss
Three predictions of reverse transcriptase (RT) mediated intron loss were fulfilled among the observed intron losses in P. falciparum and T. parva (i.e., positions at which introns are present in 2 out of 3 species). First, intron losses are biased toward the 3' end of the gene. Among 26 genes with at least 1 three-way-conserved intron position as well as at least 1 loss in P. falciparum, 18 showed a bias toward 3' loss (P = 0.038; see Roy and Gilbert 2005a for a thorough discussion). For T. parva losses, 6/8 genes showed 3'-biased loss (not statistically significant). Second, genes experiencing multiple intron losses showed a bias toward loss of adjacent introns. For all 10 genes with at least 1 intron position conserved across all 3 species and at least 2 intron losses in P. falciparum, the lost introns were adjacent relative to the conserved introns (P = 0.0015; see Roy and Gilbert 2005a for a thorough discussion). For Theileria multiple losses were adjacent in 1/3 cases (not statistically significant). Third, 99% (451/456 in P. falciparum; 59/60 in T. parva) of observed intron losses were exact (not associated with coding sequence alignment gaps between intron-containing and -lacking homologs), as expected by RT-mediated intron loss.
No Intron Loss or Gain Between C. parvum and C. hominis
We also studied intron evolution in Cryptosporidium. All 164 predicted C. parvum introns in conserved regions were found to be present in closely related C. hominis; thus there has been no intron loss in C. hominis nor intron gain in C. parvum since the species' divergence. Silent site divergence between C. parvum and C. hominis is approximately 2% (Xu et al. 2004), suggesting a date of divergence of roughly 2 Mya (assuming the estimated divergence rate in Plasmodium of around 5 x 10–9 per year; Neafsey, Hartl, and Berriman 2005; Tanabe et al. 2004). Lack of intron gain in 2 My in 3,396 C. parvum genes suggests a rate of less than 1 intron gain per gene per 7 By, within the range of estimates for other eukaryotic lineages (e.g., Roy, Fedorov, and Gilbert 2003; Nielsen et al. 2004; Lin et al. 2006; Stajich and Dietrich 2006).
It is not known why nearly intronless species retain their few remaining introns. One possibility is that retained introns encode essential functions (e.g., Jeffares, Mourier, and Penny 2006), in which case we might expect them to be highly conserved evolutionarily. Interestingly, of 109 C. parvum intron positions in conserved regions, a much smaller fraction (36.7%) were shared with T. gondii than for either of the more intron-rich species (70.6% in T. parva, 71.6% in Plasmodium; P < 10–11 by a Fisher Exact test), even when C. parvum introns that fell near (within 5 codons of) T. gondii intron positions were considered shared (51.4%; P = 1 x 10–4). An example of a highly diverged C. parvum intron-exon structure is given in figure 5. Thus, C. parvum introns are less evolutionarily conserved than are introns in other apicomplexans.
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Discussion |
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Intron Loss/Gain Evolution in the Evolutionary History of Plasmodium and Theileria
We report large-scale conservation of intron positions in Plasmodium and Theileria with the outgroup T. gondii and pronounced excesses of intron loss over intron gain in both Plasmodium and Theileria. For both P. falciparum and T. parva, more than 70% of introns in conserved regions were also present in T. gondii; thus the vast majority of introns in these species predate the Plasmodium-Theileria divergence. The Plasmodium-Theileria ancestor was more intron rich than species from either genera, with an estimated 4.5 times as many introns as P. falciparum and 38% more introns than Theileria. Overall, we estimate that intron losses have outnumbered gains in the lineage leading to T. parva by some 5.8 to 1, and in P. falciparum by an astounding 56 to 1. These results are in good qualitative agreement with a previous analysis based on a smaller number of genes, which estimated that the ancestor was 5.5 times as intron rich as P. falciparum and had 30% more introns than T. parva, with a pronounced excess of losses in Theileria and an overwhelming excess in Plasmodium since the ancestor (Nguyen et al. 2007
). This picture is consistent with our increasingly clear picture that early eukaryotes harbored large numbers of introns and a complex spliceosome (Fedorov et al. 2002; Rogozin et al. 2003; Collins and Penny 2005; Roy and Gilbert 2005b; Carmel et al. 2007).
Evidence for Retrotransposons in Ancient Apicomplexans
The pattern of intron loss in Plasmodium and Theileria strongly suggests intron loss by recombination with reverse transcribed copies of spliced mRNAs. Most strikingly, the vast majority of intron losses in both lineages are exact, occurring without addition or deletion of adjacent coding sequence. This pattern is expected based on reverse-transcribed mRNA-mediated loss, but is not expected based on simple genomic deletion (Roy and Gilbert 2005a). Second, intron losses in both lineages tend to be 3' biased, consistent with the 3' bias of reverse-transcribed products (Mourier and Jeffares 2003; Sverdlov et al. 2004; Roy and Gilbert 2005a). Finally, introns in genes experiencing multiple losses in the same lineage tend to fall adjacent to each other along the gene, consistent with loss of multiple adjacent introns via double recombination involving nonadjacent exons (Niu, Hou, and Li 2005; Stajich and Dietrich 2006). In total, these patterns provide strong evidence for the presence and activity of retrotransposons in the ancestry of Theileria and Plasmodium. These findings are striking in light of the (near) absence of these elements in modern lineages (Nene, Morzaria, and Bishop 1998; Gardner et al. 2002; Figueiredo et al. 2005; Durand, Oelofse, and Coetzer 2006; S.W. Roy and D.L. Hartl unpublished results), as reinforced by the near absence of intron loss in the recent history of both genera (Roy and Hartl 2006; Roy and Penny 2006). The implied evolutionary history of these genera is shown in figure 6.
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A Possible Cause for Retroelement Reduction in Plasmodium and Theileria
What explains the apparent reduction in retrotransposons in Plasmodium and Theileria? Theory has shown that transposable elements are expected to proliferate so long as the selection against a transposable element is less than the rate of transposition (Charlesworth, Sniegowski, and Stephan 1994
). Selection against a transposable element may then be divided into such components as selection against the presence of the physical transposable element sequence in the genome, selection against ectopic recombinations between transposable element copies, and selection against additional transpositions (Charlesworth, Sniegowski, and Stephan 1994).
For most species, this last factor may be rather minimal. For species with large fractions of nonfunctional sequence, most newly inserted transposable element copies are likely to have little functional consequence. In addition, for species with frequent outcrossing, meiotic recombination will rapidly dissociate the progenitor copy from a deleterious descendent insertion, diminishing the total selective effect on the progenitor copy (a more complete treatment will be presented elsewhere; Hickey 1982). However, for species with compact genomes and with infrequent outcrossing, such selection may be sufficient to prohibit proliferation of transposable elements.
Plasmodium and Theileria species may fit both of these criteria. Plasmodium species, for instance, undergo 1 mitotic event (giving rise to dozens of individuals from a single parent) every few days, but undergo only 1 meiotic event perhaps every 6 months. Thus there is only 1 sexual recombination event per 100–200 asexual "generations." Moreover, due to the life cycle of the parasite, meiotic events often involve individuals of like genotype, which will not dissociate the progenitor transposable element locus from a descendent copy. In addition, P. falciparum has high gene density, with 9.7 Mb of predicted coding sequence out of a total genome sequence of 22 Mb (Gardner et al. 2002). Conditions are similar for Theileria. Including functional non-protein-coding sequences, likely more than half of Plasmodium genome is composed of functional sequence.
One possible explanation for the reduction of retrotransposons (activity) in Plasmodium and Theileria, then, could be reduction in noncoding sequences. Apicomplexans, like many intracellular parasites, have undergone genomic reduction of various kinds, including gene loss and intron loss (Keeling 2004). If in addition both Plasmodium and Theileria have undergone reduction in nonfunctional sequences (or more precisely, to have increased the fraction of their sequence which is functional), this change could have moved both genera over the threshold to nonproliferation of transposable elements. This could have led to a stark reduction in retrotransposon activity and, thus, to the observed near-cessation of intron loss. Future theoretical work should explore this possibility.
Cause and Effect in Genome Structure Evolution
These findings underscore the complex relationships between the evolution of different genomic structures. In this case, genomic reduction in 1 kind of noncoding element, retrotransposons, appears to have led to the retention (or recent lack of loss) of another kind of noncoding element, introns, likely due to reduction in the rate of retrotranscriptase-mediated intron loss mutations (Roy and Hartl 2006; Roy and Penny 2006). This is a result of the web of dependency between elements in genome evolution: (1) retroelement activity is important for intron loss and perhaps intron gain, while intron sequences represent important sites for transposable element insertions; (2) recombination is necessary for intron loss, as well as for transposable element propagation; (3) transposable elements are an important source of intergenic and intronic sequences and are dependent on these noncoding sequences for propagation. These interconnections underscore the difficulties with a simple notion of "genomic complexity."
The Causes of Intron Evolution
Following our previous arguments (Roy and Gilbert 2006; Roy and Hartl 2006; Roy and Penny 2006), we have put forward an essentially mutation-based explanation for observed heterogeneity of rates. This is in contrast to the suggestion of Nguyen, Yoshihama, and Kenmochi (2007), who suggested that periods of rapid intron loss/gain evolution may be associated with evolutionary transitions. While we find this an interesting possibility, we do not see much evidence for it currently. The previous authors' data essentially shows a large number of gain/loss events over most of the tree, with the exception of 3 periods within apicomplexan evolution: recent Plasmodium and Theileria evolution and 1 deep branch. The vast majority of the branches studied by Nguyen and coauthors are very long with respect to intron loss/gain – of the outgroups to the Toxoplasma-Theileria divergence, they estimate that between 56% and 98% of ancestral introns have been lost along each branch. Under such circumstances it will be very difficult to accurately estimate loss/gain rates, particularly given uncertainties associated with divergence date estimates. Indeed, we have recently shown that a previous study that provided evidence for an association between intron loss and gain and epochs of rapid evolutionary change may have been unable to accurately reconstruct intron loss/gain due to the presence of very long branches in their sample (Roy and Penny 2007). Further work should seek to test this intriguing idea.
Intron Evolution in Cryptosporidium
We also report the first study of intron loss/gain evolution in nearly intronless Cryptosporidium species. We find no evidence for ongoing intron loss (no loss in 2 My, although the short evolutionary time makes firm conclusions difficult). We also find no intron gains in 2 My, suggesting a rate less than 1 gain per gene per 7 By.
By contrast, we find low levels of conservation of C. parvum introns with intron-rich T. gondii. An increasing number of instances of near-complete intron loss in eukaryotes have been documented; however no intronless eukaryotes have yet been found. It is not known why nearly intronless species retain their few introns. One possibility is that the few remaining introns represent a subset of functionally important introns whose loss is opposed by selection. That C. parvum introns are not highly evolutionarily shared suggests against this possibility.
How may this result be explained? Since both intron loss and gain are likely to be dependent on transposable element activity, rates of intron loss and gain might be expected to be directly correlated. In this case, lineages such as Cryptosporidium which have experienced a high degree of loss might also have experienced a relatively high rate of gain, leading to a generally lower level of intron conservation than for other lineages.
Conclusions
We report genome-wide analyses indicating: (1) a high degree conservation of Theileria and Plasmodium intron positions with the coccid T. gondii, (2) a striking dominance of intron loss over gain in Theileria and Plasmodium since their divergence, (3) complete conservation of C. parvum introns in C. hominis, and (4) low levels of conservation of C. parvum introns in T. gondii. These results reinforce the notion of intron number reduction as a very common evolutionary pattern and focus attention on the intriguing patterns of intron evolution in the many nearly intronless eukaryotic lineages.
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Footnotes |
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Geoffrey McFadden, Associate Editor
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References |
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Abrahamsen MS, Templeton TJ, Enomoto S, et al, (20 co-authors). Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 304:441–445.
Aparicio S, Chapman J, Stupka E, et al, (41 co-authors). Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 297:1301–1310.
Carmel L, Wolf YI, Rogozin IB, Koonin EV. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 17:1034–1044.
Charlesworth B, Sniegowski P, Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature (1994) 371:215–220.[CrossRef][Medline]
Collins L, Penny D. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol. (2005) 22:1053–1066.
Csuros M. Likely scenarios of intron evolution. In: Comparative genomics. Volume 3678 of LNBI—McLysaght A, Huson DH, eds. (2005) Heidelberg: Springer-Verlag. 47–60.
Durand PM, Oelofse AJ, Coetzer TL. An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome. BMC Genomics (2006) 7:282.[CrossRef][Medline]
Escalante AA, Ayala FJ. Evolutionary origin of Plasmodium and other Apicomplexa based on rRNA genes. Proc Natl Acad Sci USA (1995) 92:5793–5797.
Fedorov A, Merican AF, Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genomes. Proc Natl Acad Sci USA (2002) 99:16128–16133.
Figueiredo LM, Rocha EPC, Mancio-Silva L, Prevost C, Hernandez-Verdun D, Scherf A. The unusually large Plasmodium telomerase reverse transcriptase localizes in a discrete compartment associated with the nucleolus. Nucleic Acids Res. (2005) 33:1111–1122.
Gardner MJ, Bishop R, Shah T, et al, (44 co-authors). Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 309:134–137.
Gardner MJ, Hall N, Fung E, et al, (45 co-authors). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 419:498–511.[CrossRef][Medline]
Gilson PR, McFadden GI. The miniaturized nuclear genome of eukaryotic endosymbion contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns. Proc Natl Acad Sci USA (1996) 93:7737–7742.
Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus. Proc Natl Acad Sci USA (2006) 103:9566–9571.
Hickey DA. Selfish DNA: a sexually-transmitted nuclear parasite. Genetics (1982) 101:519–531.
Jeffares DC, Mourier T, Penny D. The biology of intron gain and loss. Trends Genet. (2006) 22:16–22.[CrossRef][Web of Science][Medline]
Katinka MD, Duprat S, Cornillot E, et al, (17 co-authors). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature (2001) 414:450–453.[CrossRef][Medline]
Keeling PJ. Reduction and compaction in the genome of the apicomplexan parasite Cryptosporidium parvum. Dev Cell. (2004) 6:614–616.[CrossRef][Web of Science][Medline]
Lander ES, Linton LM, Birren B, et al, (256 co-authors). Initial sequencing and analysis of the human genome. Nature (2001) 409:860–921.[CrossRef][Medline]
Lin H, Zhu W, Silva J, Gu X, Buell CR. Intron gain and loss in segmentally duplicated genes in rice. Genome Biol. (2006) 7:R41.[CrossRef][Medline]
Mourier T, Jeffares DC. Eukaryotic intron loss. Science (2003) 300:1393.
Neafsey DE, Hartl DL, Berriman M. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Biol Evol. (2005) 22:1621–1626.
Nene V, Morzaria S, Bishop R. Organisation and informational content of the Theileria parva genome. Mol Biochem Parasitol (1998) 95:1–8.[CrossRef][Web of Science][Medline]
Nguyen HD, Yoshihama M, Kenmochi N. New maximum likelihood estimators for eukaryotic intron evolution. PLoS Comput Biol. (2005) 1:e79.[CrossRef][Medline]
Nguyen HD, Yoshihama M, Kenmochi N. The evolution of spliceosomal introns in Alveolates. Mol Biol Evol. (2007) 24:1093–1096.
Nielsen CB, Friedman B, Birren B, Burge CB, Galagan JE. Patterns of intron gain and loss in fungi. PLoS Biol (2004) 2:e422.[CrossRef][Medline]
Niu DK, Hou WR, Li SW. mRNA-mediated intron losses: evidence from extraordinarily large exons. Mol Biol Evol. (2005) 22:1475–1481.
Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV. Remarkable interkingdom conservation of intron positions and massive, lineage specific intron loss and gain in eukaryotic evolution. Curr Biol. (2003) 13:1512–1517.[CrossRef][Web of Science][Medline]
Roy SW, Fedorov A, Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci USA (2003) 100:7158–7162.
Roy SW, Gilbert W. The pattern of intron loss. Proc Natl Acad Sci USA (2005a) 102:1986–1991.
Roy SW, Gilbert W. Complex early genes. Proc Natl Acad Sci USA (2005b) 102:1986–1991.
Roy SW, Gilbert W. Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci USA (2005c) 102:5773–5778.
Roy SW, Gilbert W. The evolution of spliceosomal introns: patterns, puzzles, and progress. Nat Rev Genet. (2006) 7:211–221.[CrossRef][Web of Science][Medline]
Roy SW, Hartl DL. Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number. Genome Res. (2006) 16:750–756.
Roy SW, Penny D. Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res. (2006) 16:1270–1275.
Roy SW, Penny D. On the incidence of intron loss and gain in paralogous gene families. Mol Biol Evol. (2007) 24:1579–1581.
Sakharkar KR, Dhar PK, Chow VT. Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol. (2004) 54:1937–1941.
Slamovits CH, Keeling PJ. A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol Biol. (2006) 6:34.[CrossRef][Medline]
Stajich JE, Dietrich FS. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryotic Cell. (2006) 5:789–793.
Sverdlov AV, Babenko VN, Rogozin IB, Koonin EV. Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene (2004) 338:85–91.[CrossRef][Web of Science][Medline]
Tanabe K, Sakihama N, Hattori T, Ranford-Cartwright L, Goldman I, Escalante AA, Lal AA. Genetic distance in housekeeping genes between Plasmodium falciparum and Plasmodium reichenowi and within P. falciparum. J Mol Evol. (2004) 59:687–694.[CrossRef][Web of Science][Medline]
Xu P, Widmer G, Wang Y, et al, (18 co-authors). The genome of Cryptosporidium hominis. Nature (2004) 431:1107–1112.[CrossRef][Medline]
Yu J, Hu S, Wang J, et al, (100 co-authors). A draft sequence of the rice genome. (Oryza sativa L. ssp. Indica). Science (2002) 296:79–92.
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