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Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi.

Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M, Gabaldón T, Pisabarro AG, Oguiza JA, Ramírez L - BMC Genomics (2014)

Bottom Line: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes.P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments.The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

View Article: PubMed Central - PubMed

Affiliation: Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain. lramirez@unavarra.es.

ABSTRACT

Background: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.

Results: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.

Conclusion: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

No MeSH data available.


Related in: MedlinePlus

Helitrons break the synteny between theP. ostreatusPC15 and PC9 genomes. The distribution of helitrons in the chromosomes of the dikaryotic strain N001 is shown in A (PC15 elements are shown in blue and in PC9 elements are shown in red). Truncated elements are marked with a ‘*’. An ACT [32] comparison of the squared region between PC15 and PC9 is shown in B. The lack of gene colinearity between PC9 and PC15 in the squared region of chromosomeVII is shown in C (coordinates: 1,528,715-1,479,715). In the synteny plot, coding regions are represented in purple, and inter-genic regions in pink. Arrows labeled IR represent the inverted repeats found in a 37.2 kb region duplicated in PC15 and absent in PC9 genome. Blue arrows underneath synteny plot represent predicted genes.
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Fig3: Helitrons break the synteny between theP. ostreatusPC15 and PC9 genomes. The distribution of helitrons in the chromosomes of the dikaryotic strain N001 is shown in A (PC15 elements are shown in blue and in PC9 elements are shown in red). Truncated elements are marked with a ‘*’. An ACT [32] comparison of the squared region between PC15 and PC9 is shown in B. The lack of gene colinearity between PC9 and PC15 in the squared region of chromosomeVII is shown in C (coordinates: 1,528,715-1,479,715). In the synteny plot, coding regions are represented in purple, and inter-genic regions in pink. Arrows labeled IR represent the inverted repeats found in a 37.2 kb region duplicated in PC15 and absent in PC9 genome. Blue arrows underneath synteny plot represent predicted genes.

Mentions: A total of 37 validated helitrons in the HELPO1 and HELPO2 families were detected in the PC15 strain (Figure 3A, Table 1), accounting for 0.35% of the total genome size. Among these helitrons, 19 were intact elements, 11 out of the 19 were full-length putative autonomous elements, and the remaining elements were truncated copies. In the PC9 genome, 10 helitrons accounting for 0.05% of its genome were found, of which only five could be mapped to the corresponding PC15 scaffolds (Figure 3A). Five elements showed intact 5′ and 3′ boundaries, one was putative autonomous (HELPO1.1), and the rest were truncated elements.Figure 3


Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi.

Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M, Gabaldón T, Pisabarro AG, Oguiza JA, Ramírez L - BMC Genomics (2014)

Helitrons break the synteny between theP. ostreatusPC15 and PC9 genomes. The distribution of helitrons in the chromosomes of the dikaryotic strain N001 is shown in A (PC15 elements are shown in blue and in PC9 elements are shown in red). Truncated elements are marked with a ‘*’. An ACT [32] comparison of the squared region between PC15 and PC9 is shown in B. The lack of gene colinearity between PC9 and PC15 in the squared region of chromosomeVII is shown in C (coordinates: 1,528,715-1,479,715). In the synteny plot, coding regions are represented in purple, and inter-genic regions in pink. Arrows labeled IR represent the inverted repeats found in a 37.2 kb region duplicated in PC15 and absent in PC9 genome. Blue arrows underneath synteny plot represent predicted genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289320&req=5

Fig3: Helitrons break the synteny between theP. ostreatusPC15 and PC9 genomes. The distribution of helitrons in the chromosomes of the dikaryotic strain N001 is shown in A (PC15 elements are shown in blue and in PC9 elements are shown in red). Truncated elements are marked with a ‘*’. An ACT [32] comparison of the squared region between PC15 and PC9 is shown in B. The lack of gene colinearity between PC9 and PC15 in the squared region of chromosomeVII is shown in C (coordinates: 1,528,715-1,479,715). In the synteny plot, coding regions are represented in purple, and inter-genic regions in pink. Arrows labeled IR represent the inverted repeats found in a 37.2 kb region duplicated in PC15 and absent in PC9 genome. Blue arrows underneath synteny plot represent predicted genes.
Mentions: A total of 37 validated helitrons in the HELPO1 and HELPO2 families were detected in the PC15 strain (Figure 3A, Table 1), accounting for 0.35% of the total genome size. Among these helitrons, 19 were intact elements, 11 out of the 19 were full-length putative autonomous elements, and the remaining elements were truncated copies. In the PC9 genome, 10 helitrons accounting for 0.05% of its genome were found, of which only five could be mapped to the corresponding PC15 scaffolds (Figure 3A). Five elements showed intact 5′ and 3′ boundaries, one was putative autonomous (HELPO1.1), and the rest were truncated elements.Figure 3

Bottom Line: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes.P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments.The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

View Article: PubMed Central - PubMed

Affiliation: Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain. lramirez@unavarra.es.

ABSTRACT

Background: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.

Results: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.

Conclusion: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.

No MeSH data available.


Related in: MedlinePlus