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Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes.

Da Lage JL, Binder M, Hua-Van A, Janeček S, Casane D - BMC Evol. Biol. (2013)

Bottom Line: The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome.There was little variation of intron size.Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Evolution, génomes et spéciation UPR 9034 CNRS, 91198 Gif-sur-Yvette, and Université Paris-Sud, Orsay, 91405, France. jldl@legs.cnrs-gif.fr

ABSTRACT

Background: Increasing genome data show that introns, a hallmark of eukaryotes, already existed at a high density in the last common ancestor of extant eukaryotes. However, intron content is highly variable among species. The tempo of intron gains and losses has been irregular and several factors may explain why some genomes are intron-poor whereas other are intron-rich.

Results: We studied the dynamics of intron gains and losses in an α-amylase gene, whose product breaks down starch and other polysaccharides. It was transferred from an Actinobacterium to an ancestor of Agaricomycotina. This gene underwent further duplications in several species. The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome. A number of these oldest introns, regularly scattered along the gene, remained conserved. Subsequent gains and losses were lineage dependent, with a majority of losses. Moreover, a few species exhibited a high number of both specific intron gains and losses in recent periods. There was little sequence conservation around insertion sites, then probably little information for splicing, whereas splicing sites, inside introns, showed typical and conserved patterns. There was little variation of intron size.

Conclusions: Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.

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Related in: MedlinePlus

Reconstitution of intron gain and loss events mapped on a species tree. Branch lengths are proportional to time, the time scale in million years is shown below. Numbers along the branches are intron positions. HGT: horizontal transfer event. Black numbers: intron gains; red numbers: intron losses in all gene copies in a clade; green numbers: intron loss in some, but not all gene copies in a clade; blue numbers: intron gains specific to Stehi1/78757/. Black crosses show complete gene losses.
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Figure 3: Reconstitution of intron gain and loss events mapped on a species tree. Branch lengths are proportional to time, the time scale in million years is shown below. Numbers along the branches are intron positions. HGT: horizontal transfer event. Black numbers: intron gains; red numbers: intron losses in all gene copies in a clade; green numbers: intron loss in some, but not all gene copies in a clade; blue numbers: intron gains specific to Stehi1/78757/. Black crosses show complete gene losses.

Mentions: In order to reconstruct the history of intron insertions and losses, we ideally should map the intron gain and loss events onto the gene tree, applying a parsimonious or maximum likelihood model. We tried to apply a parsimony analysis on the unmodified gene tree using Mesquite v2.75 [61]. This led to at least 23 occurrences of parallel gains, counting parallel gains as the number of gain events at a given intron position, minus one. We obtained a similar result in a maximum likelihood analysis, parametered with a bias of gains over losses of 1:10 (not shown). Actually, the gene tree built from our data (Additional file 5: Figure S2) had a number of weakly supported nodes and was incongruent with the currently known species phylogeny, and thus failed to clarify the history of the gene family since the time it was transferred into an ancestral genome. High divergence between gene copies, multiple independent duplications and paralog losses may have obscured the phylogenetic signal. HGT may also have occurred between fungal species (see e.g. ref. [66]). However, our data show no clear evidence for this, except for Bjerkandera adusta (see below). Studying synteny among species (Mycocosm website) was no more helpful to uncover orthology relationships, because of quick loss of synteny, except in closely related species. Therefore, we attempted to reconcile the gene tree with the known phylogeny using the Notung software [62]. We obtained a complex history, with 19 duplications and 56 gene losses (default parameters, with rearrangement option and rooting with Stehi1/78757/, Additional file 6: Figure S3). Moreover, some major branches were marked as weak by the program. This may be due to the low support values at a majority of nodes (Additional file 5: Figure S2). Therefore, we mapped the intron gains and losses on a species tree (Figure 3) from the data of Figure 2, in a weighted parsimony framework. With this method, the possible parallel gains were limited to positions 2, 4, 21 and 24. Intron gains were rather easily inferred. Clearly, there has been a relatively rapid invasion of the primarily intronless gene by introns after its transfer into the ancestral genome. According to our reconstruction, 17 extant introns are ancestral, since they are still shared together by the single copy of the early branching-off Dacryopinax sp. and a number of other species. Among them, 9 are still widely distributed. Note that Dacryopinax sp. has three specific introns. We considered those introns as specific gains, but this cannot be ascertained without additional data from other early diverging species. To infer intron losses, when several copies were present in a species, for each intron position, we distinguished between intron losses in all gene copies, and intron losses in some, but not all gene copies. Intron losses in all copies were counted as a single event, because it was rarely possible to discriminate between parallel losses in paralogs and a single event prior to duplication, thus probably underestimating the rate of loss. Some examples for which the gene tree was clear enough to allow more precise reconstitution of the loss events, were e.g. partial losses of introns 34 and 39 in Ganoderma sp. and its relative Dichomitus squalens, or independent losses at positions 33 and 34 in G. trabeum Glotr1/121909/ and P. strigosozonata Punst1/74571/. Figure 3 shows that the same set of introns (1, 6, 19, 20, 33, 42, 45) was lost twice, at two internal nodes, the node basal to Agarics and the node basal to Polypores. This intriguing result of our reconstruction might reveal hidden paralogy, but the gene tree was not clear enough to validate this possibility. Indeed, parallel losses were observed many times in this study, and are generally considered to be much more frequent than parallel gains. However, it seems unlikely that such a co-occurrence of parallel losses may have occurred by chance. On the other hand, the Notung reconciliation assay was not consistent in this respect, because it did not propose to group as orthologs the two clades that have lost this set of introns, as would be expected if we infer a single occurrence of the loss of the seven introns. Similarly, we considered that another set of introns (8, 34, 39, 44, 50, 56) was lost independently along two external branches, Piriformospora indica and Auricularia delicata. Simulation (100,000 trials) suggested that the probability of such 6 parallel losses among eight intron losses in a pool of 20 introns was about 1%, at most 3% when considering that some positions were lost more frequently (estimated by the actual rate observed in our data set). In the case of these two species, the gene tree suggested a relationship between the single-copy genes present in both species. This could represent the remnant gene copy of two ancestral copies, which was lost in the ingroup clade, whereas, on the contrary, the remaining ingroup copy would have been lost in those two species. Note that the Notung reconciliation suggests an ortholog relationship of these two genes too. Then, possible hidden paralogy leads to overestimating the rate of losses.


Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes.

Da Lage JL, Binder M, Hua-Van A, Janeček S, Casane D - BMC Evol. Biol. (2013)

Reconstitution of intron gain and loss events mapped on a species tree. Branch lengths are proportional to time, the time scale in million years is shown below. Numbers along the branches are intron positions. HGT: horizontal transfer event. Black numbers: intron gains; red numbers: intron losses in all gene copies in a clade; green numbers: intron loss in some, but not all gene copies in a clade; blue numbers: intron gains specific to Stehi1/78757/. Black crosses show complete gene losses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3584928&req=5

Figure 3: Reconstitution of intron gain and loss events mapped on a species tree. Branch lengths are proportional to time, the time scale in million years is shown below. Numbers along the branches are intron positions. HGT: horizontal transfer event. Black numbers: intron gains; red numbers: intron losses in all gene copies in a clade; green numbers: intron loss in some, but not all gene copies in a clade; blue numbers: intron gains specific to Stehi1/78757/. Black crosses show complete gene losses.
Mentions: In order to reconstruct the history of intron insertions and losses, we ideally should map the intron gain and loss events onto the gene tree, applying a parsimonious or maximum likelihood model. We tried to apply a parsimony analysis on the unmodified gene tree using Mesquite v2.75 [61]. This led to at least 23 occurrences of parallel gains, counting parallel gains as the number of gain events at a given intron position, minus one. We obtained a similar result in a maximum likelihood analysis, parametered with a bias of gains over losses of 1:10 (not shown). Actually, the gene tree built from our data (Additional file 5: Figure S2) had a number of weakly supported nodes and was incongruent with the currently known species phylogeny, and thus failed to clarify the history of the gene family since the time it was transferred into an ancestral genome. High divergence between gene copies, multiple independent duplications and paralog losses may have obscured the phylogenetic signal. HGT may also have occurred between fungal species (see e.g. ref. [66]). However, our data show no clear evidence for this, except for Bjerkandera adusta (see below). Studying synteny among species (Mycocosm website) was no more helpful to uncover orthology relationships, because of quick loss of synteny, except in closely related species. Therefore, we attempted to reconcile the gene tree with the known phylogeny using the Notung software [62]. We obtained a complex history, with 19 duplications and 56 gene losses (default parameters, with rearrangement option and rooting with Stehi1/78757/, Additional file 6: Figure S3). Moreover, some major branches were marked as weak by the program. This may be due to the low support values at a majority of nodes (Additional file 5: Figure S2). Therefore, we mapped the intron gains and losses on a species tree (Figure 3) from the data of Figure 2, in a weighted parsimony framework. With this method, the possible parallel gains were limited to positions 2, 4, 21 and 24. Intron gains were rather easily inferred. Clearly, there has been a relatively rapid invasion of the primarily intronless gene by introns after its transfer into the ancestral genome. According to our reconstruction, 17 extant introns are ancestral, since they are still shared together by the single copy of the early branching-off Dacryopinax sp. and a number of other species. Among them, 9 are still widely distributed. Note that Dacryopinax sp. has three specific introns. We considered those introns as specific gains, but this cannot be ascertained without additional data from other early diverging species. To infer intron losses, when several copies were present in a species, for each intron position, we distinguished between intron losses in all gene copies, and intron losses in some, but not all gene copies. Intron losses in all copies were counted as a single event, because it was rarely possible to discriminate between parallel losses in paralogs and a single event prior to duplication, thus probably underestimating the rate of loss. Some examples for which the gene tree was clear enough to allow more precise reconstitution of the loss events, were e.g. partial losses of introns 34 and 39 in Ganoderma sp. and its relative Dichomitus squalens, or independent losses at positions 33 and 34 in G. trabeum Glotr1/121909/ and P. strigosozonata Punst1/74571/. Figure 3 shows that the same set of introns (1, 6, 19, 20, 33, 42, 45) was lost twice, at two internal nodes, the node basal to Agarics and the node basal to Polypores. This intriguing result of our reconstruction might reveal hidden paralogy, but the gene tree was not clear enough to validate this possibility. Indeed, parallel losses were observed many times in this study, and are generally considered to be much more frequent than parallel gains. However, it seems unlikely that such a co-occurrence of parallel losses may have occurred by chance. On the other hand, the Notung reconciliation assay was not consistent in this respect, because it did not propose to group as orthologs the two clades that have lost this set of introns, as would be expected if we infer a single occurrence of the loss of the seven introns. Similarly, we considered that another set of introns (8, 34, 39, 44, 50, 56) was lost independently along two external branches, Piriformospora indica and Auricularia delicata. Simulation (100,000 trials) suggested that the probability of such 6 parallel losses among eight intron losses in a pool of 20 introns was about 1%, at most 3% when considering that some positions were lost more frequently (estimated by the actual rate observed in our data set). In the case of these two species, the gene tree suggested a relationship between the single-copy genes present in both species. This could represent the remnant gene copy of two ancestral copies, which was lost in the ingroup clade, whereas, on the contrary, the remaining ingroup copy would have been lost in those two species. Note that the Notung reconciliation suggests an ortholog relationship of these two genes too. Then, possible hidden paralogy leads to overestimating the rate of losses.

Bottom Line: The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome.There was little variation of intron size.Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire Evolution, génomes et spéciation UPR 9034 CNRS, 91198 Gif-sur-Yvette, and Université Paris-Sud, Orsay, 91405, France. jldl@legs.cnrs-gif.fr

ABSTRACT

Background: Increasing genome data show that introns, a hallmark of eukaryotes, already existed at a high density in the last common ancestor of extant eukaryotes. However, intron content is highly variable among species. The tempo of intron gains and losses has been irregular and several factors may explain why some genomes are intron-poor whereas other are intron-rich.

Results: We studied the dynamics of intron gains and losses in an α-amylase gene, whose product breaks down starch and other polysaccharides. It was transferred from an Actinobacterium to an ancestor of Agaricomycotina. This gene underwent further duplications in several species. The results indicate a high rate of intron insertions soon after the gene settled in the fungal genome. A number of these oldest introns, regularly scattered along the gene, remained conserved. Subsequent gains and losses were lineage dependent, with a majority of losses. Moreover, a few species exhibited a high number of both specific intron gains and losses in recent periods. There was little sequence conservation around insertion sites, then probably little information for splicing, whereas splicing sites, inside introns, showed typical and conserved patterns. There was little variation of intron size.

Conclusions: Since most Basidiomycetes have intron-rich genomes and this richness was ancestral in Fungi, long before the transfer event, we suggest that the new gene was shaped to comply with requirements of the splicing machinery, such as short exon and intron sizes, in order to be correctly processed.

Show MeSH
Related in: MedlinePlus