MBE Advance Access originally published online on August 30, 2006
Molecular Biology and Evolution 2006 23(12):2259-2262; doi:10.1093/molbev/msl098
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Letters |
Smoke Without Fire: Most Reported Cases of Intron Gain in Nematodes Instead Reflect Intron Losses
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
E-mail: scottwroy{at}gmail.com.
| Abstract |
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Identification of recently gained spliceosomal introns would provide crucial evidence in the continuing debate concerning the age and evolutionary significance of introns. A previously published genomic analysis reported to have identified 122 introns that had been gained since the divergence of the nematodes Caenorhabidits elegans and Caenorhabditis briggsae
100 MYA. However, using newly available genomic sequence from additional Caenorhabditis species, we show that 74% (60/81) of the reported gains in C. elegans are present in a C. briggsae relative. This pattern indicates that these introns represent losses in C. briggsae, not gains in C. elegans. In addition, 61% (25/41) of the reported gains in C. briggsae are present in the more distant C. briggsae relative, in a pattern suggesting that additional reported gains in C. elegans and/or C. briggsae may in fact represent unrecognized losses. These results underscore the dominance of intron loss over intron gain in recent eukaryotic evolution, the pitfalls associated with parsimony in inferring intron gains, and the importance of genomic sequencing of clusters of closely related species for drawing accurate inferences about genome evolution.
Key Words: intron gain genome complexity genome annotation genome sequencing genome evolution parsimony
The origin of the splicesomal introns of eukaryotes constitutes a 30-year-old mystery (de Souza 2003
; Jeffares et al. 2006
; Martin and Koonin 2006
; Rodríguez-Trelles et al. 2006
; Roy and Gilbert 2006
). In 1998, Logsdon et al. laid out conditions for determining the source of a recently gained intron: 1) strong evidence for the intron's recent gain, derived from "dense phylogenetic sampling"; and 2) the "molecular smoking gun"an intronic sequence whose clear similarity to another genetic element betrays the intron's origin. The subsequent years have been an extremely active time for the study of intron evolution (Tarrío et al. 1998
, 2003
; Venkatesh et al. 1999
; Sakharkar et al. 2001
; Seo et al. 2001
; Wolf et al. 2001
; Fedorov et al. 2002
; Llopart et al. 2002
; Wada et al. 2002
; Bon et al. 2003
; Fedorov et al. 2003
; Rogozin et al. 2003
; Nielsen et al. 2004
; Slamovits and Keeling 2006
). However, until 2004 only a single clearly characterized intron gain had been reported (Iwamoto 1998
). Then finally, 2 years ago Coghlan and Wolfe (2004)
reported the cases of 81 potentially recently gained introns in Caenorhabditis elegans and 41 in Caenorhabditis briggsae. Each of the 122 introns was not found in the other Caenorhabditis species or in various outgroups (apparently fulfilling the first criterion; fig. 1), and 28 of the introns showed sequence similarity to other Caenorhabditis introns (apparently fulfilling the second). These results have been widely discussed (e.g., Roy 2004
; Rodríguez-Trelles et al. 2006
) and widely cited (>35 citations) and were hailed by Logsdon (2004) as the long-awaited "smoking gun."
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The first point of contention concerned interpretation of the intron sequences themselves (the second criterion). Coghlan and Wolfe (2004)
Here, we report evidence that many of the reported intron gains are not even true intron gains (criterion 1) but instead reflect intron losses. We examined putatively orthologous sequences from newly available genomic sequences from 2 relatives of C. briggsae: Caenorhabditis remanei and Caenorhabditis sp. 4 (fig. 1). If the 81 C. elegans introns reported to be recent gains are in fact just that, they should clearly be absent from these species. Instead, 74% (60/81) were found to be shared with one or both species (table 1, see e.g., in fig. 2; a more detailed summary is available as Supplementary Material Online). This implies that these introns' absence in C. briggsae is due to intron loss and not due to recent gain in C. elegans. The remaining 21 possible C. elegans gains may either be actual gains in C. elegans or losses in the C. briggsaeC. sp. 4 ancestor (table 1, branch ii). Thus, in most cases (at least for C. elegans), there is no smoking gun.
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Among the 41 reported C. briggsae gains, fully 61% (25) are present in C. sp. 4 and, thus, could represent gains in the C. briggsaeC. remaneiC. sp. 4 ancestor (branch ii) or losses in C. elegans. If all 25 of these introns and all 21 C. elegansspecific introns were true intron gains, there would be no losses but numerous gains in both C. elegans (branch i) and in the C. briggsaeC. sp. 4 ancestor (branch ii). This would be surprising in light of the observation of 3.75 losses per gain (60/16) in the sample occurring in C. briggsae since the C. briggsaeC. sp. 4 ancestor (branch iii). This suggests that some of the remaining possible gains may also represent unrecognized losses. Though direct estimation of the loss/gain numbers here is not possible, the ratio of losses to gains in both the C. briggsaeC. sp. 4 ancestor and in C. elegans would also equal 3.75, if there were 5.6 gains and 20.9 losses in C. elegans and 4.1 gains and 15.4 losses in the C. briggsaeC. sp. 4 ancestor. In this case, only 21% (16 + 5.6 + 4.1 = 25.7 out of 122) of the reported intron gains would represent true intron gains.
Most biases identified by Coghlan and Wolfe (2004)
among the 122 reported gains are not strong for the remaining 21 possible C. elegans gains and 16 probable C. remanei gains. Only 4/37 are found in genes involved in mRNA splicing. Only 27.0% (10/37) show sequence similarity to other introns, similar to the C. briggsae losses (25.0%, 15/60). Only the reported bias toward oocyte expression remains: among genes that contain C. elegans gains and/or probable C. briggsae gains for which oocyte expression is available (Hill et al. 2000
), 70% (16/23) are present in oocytes, more than 42% for all genes assessed (P
0.01 by a Fisher's Exact test). This bias could reflect additional undetected oocyte-biased intron losses, a higher frequency of insertion of intron-creating TE insertions into germline-expressed genes (perhaps due to more accessible chromatin structure), or a dependency of intron gain on an mRNA intermediate, as suggested by Coghlan and Wolfe (2004)
.
The suggestive biases among the introns reported by Coghlan and Wolfe (sequence similarity to other introns/TEs, gene biases toward germline expression and involvement in mRNA processing) are thus apparently a case of smoke without fire (or evidence without a crime), as these introns are primarily derived from cases of intron loss, not gain. Why should introns in one species that are lost in the other show sequence similarity to other introns/TEs? It seems likely that these sequence similarities are due to independent intronic and intergenic insertions of the same TE. If rates of intron loss and intronic TE insertion were correlated due to the dependence of both processes on local recombination rate or general DNA accessibility (chromatin structure) in the germline, the same introns that are lost in one species might tend to experience TE insertion in the other. Preferential intron loss from germline-expressed genes could reflect mRNA-mediated intron loss (Mourier and Jeffares 2003
), as could the bias toward mRNA splicing-related genes, though why splicing-associated transcripts, as opposed to proteins, should associate with the spliceosome is unclear (Coghlan and Wolfe 2004
). These surprising biases in intron loss deserve further attention.
These results highlight 3 important points. First, along many eukaryotic lineages, recent evolution has been characterized by a dominance of intron loss over intron gain (e.g., Roy et al. 2003
; Cho et al. 2004; Kiontke et al. 2004; Lin et al. 2006
; Roy and Hartl 2006
; Stajich and Dietrich 2006
): in this case, even the introns that appeared most likely to represent cases of recent gains are instead mostly due to loss. Second, these results provide an important case study of the utility of parsimony in the face of high degrees of evolutionary change. Third, these results demonstrate the importance of greater taxonomic sampling and the indispensability of sequencing additional genomes for answering even seemingly straightforward questions about genome structure and evolution.
The general dearth of clear recent intron gains continues to frustrate attempts to understand mechanisms and causes of intron creation (Roy et al. 2003
; Lin et al. 2006
; Roy and Hartl 2006
; Roy et al. 2006
; Stajich and Dietrich 2006
). These observed low intron gain rates are curious as huge numbers of introns in various eukaryotic genomes attest to substantial intron creation at some point in evolution. One possible explanation is improved policing of genome insertions in modern eukaryotes relative to early/pre-eukaryotic evolution. Investigation is ongoing.
| Methods |
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From the text and supplementary materials of Coghlan and Wolfe 2004
| Supplementary Material |
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Summary of results including for each intron, the gene name, intron number, and presence (+), absence (), or uncertainty (?) in the C. briggsae relatives is available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).
| Acknowledgements |
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We thank Manuel Irimia for constructive comments and helpful discussions during the preparation of this manuscript.
| Footnotes |
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William Martin, Associate Editor
| References |
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