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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

Transcriptional profiles of helitron-specific helicases and captured genes. Five representative RNA-seq profiles of the helitron families and subfamilies (AtoE). The gene models predicted by JGI are shown in blue. Empty arrows represent manually annotated genes. The expression of the N00, PC9 and PC15 RepHel helicases and captured genes by RT-qPCR is shown in F. The Y axis of F represents the arbitrary units (RQ ) relative to the expression of the reference gene pep.
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Fig5: Transcriptional profiles of helitron-specific helicases and captured genes. Five representative RNA-seq profiles of the helitron families and subfamilies (AtoE). The gene models predicted by JGI are shown in blue. Empty arrows represent manually annotated genes. The expression of the N00, PC9 and PC15 RepHel helicases and captured genes by RT-qPCR is shown in F. The Y axis of F represents the arbitrary units (RQ ) relative to the expression of the reference gene pep.

Mentions: The transcriptional profiles of 30 helitrons and 10 truncated RepHel helicases from the P. ostreatus PC15 and PC9 genomes were investigated in solid SMY cultures using RNA-seq in the dikaryotic strain N001 (Figure 5, Table 1). An analysis of RNA-seq reads using IGV [33] yielded different profiles for the members of different families and subfamilies (Figure 5). In most cases, the RNA-seq reads did not fit with the gene models predicted by the JGI, although we also found RNA-seq reads that mapped to regions with no annotated models, for example, capC. Helitrons in the HELPO1 family showed higher levels of transcription (based on the RPKM values of the entire helitron, including the RepHel helicase and the captured genes), in comparison with the elements belonging to the HELPO2 family. The truncated PIF1 helicases showed no transcriptional activity, with the exception of helicase ID 1079561 (on chromosome X). The HELPO1.1 subfamily displayed very high levels of expression (up to 38.64 RPKM) compared with the HELPO1.3 (maximum of 7.69 RPKM) and HELPO1.2 members (maximum of 2.41 RPKM). RT-qPCR experiments were performed using mRNA from the strains PC9, PC15 and N001 grown in submerged cultures to analyze the expression of the RepHel helicases and captured genes independently. For RepHel helicases, similar relative profiles were observed in the three strains, although the ranges of the transcriptional levels were different (Figure 5F). The RepHel helicase of HELPO1.2 was frequently the most highly expressed (0.31, 20.9 and 6.9 RQs in PC9, PC15 and N001, respectively). HELPO1.1 RepHel showed much lower expression levels (0.25, 1.8 and 0.2 RQs in PC9, PC15 and N001, respectively) and HELPO2 showed no expression in N001 and PC9 (0, 2.6 and 0 RQs in PC9, PC15 and N001, respectively). Virus-like captured genes carried by LTR/Gypsy did not show transcription in any strain, and genes of unknown function, such as capA, capA2, capB and capC, showed a strain-specific expression profile. RT-qPCR experiments performed with PC9 showed that capA was the most highly expressed gene (52.3 RQs) whereas much lower (capB and capC) or no transcription (capA2) was observed for the rest of these genes. In PC15, the highest expression values corresponded to capC and capA2 (30.4 and 22.1 RQs). In N001, capA was the most highly expressed gene, followed by capC and capA2 (8.51, 2.4 and 2.2 RQs) (Figure 5F). Clear differences were observed between the capA and capA2 transcription profiles using RT-qPCR. Because the primers were designed to amplify more than one gene with the exception of capA2, capD and capF (Additional file 6: Table S4), the transcription levels obtained were the result of the contribution of every RepHel helicase and captured gene from each helitron family.Figure 5


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)

Transcriptional profiles of helitron-specific helicases and captured genes. Five representative RNA-seq profiles of the helitron families and subfamilies (AtoE). The gene models predicted by JGI are shown in blue. Empty arrows represent manually annotated genes. The expression of the N00, PC9 and PC15 RepHel helicases and captured genes by RT-qPCR is shown in F. The Y axis of F represents the arbitrary units (RQ ) relative to the expression of the reference gene pep.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Transcriptional profiles of helitron-specific helicases and captured genes. Five representative RNA-seq profiles of the helitron families and subfamilies (AtoE). The gene models predicted by JGI are shown in blue. Empty arrows represent manually annotated genes. The expression of the N00, PC9 and PC15 RepHel helicases and captured genes by RT-qPCR is shown in F. The Y axis of F represents the arbitrary units (RQ ) relative to the expression of the reference gene pep.
Mentions: The transcriptional profiles of 30 helitrons and 10 truncated RepHel helicases from the P. ostreatus PC15 and PC9 genomes were investigated in solid SMY cultures using RNA-seq in the dikaryotic strain N001 (Figure 5, Table 1). An analysis of RNA-seq reads using IGV [33] yielded different profiles for the members of different families and subfamilies (Figure 5). In most cases, the RNA-seq reads did not fit with the gene models predicted by the JGI, although we also found RNA-seq reads that mapped to regions with no annotated models, for example, capC. Helitrons in the HELPO1 family showed higher levels of transcription (based on the RPKM values of the entire helitron, including the RepHel helicase and the captured genes), in comparison with the elements belonging to the HELPO2 family. The truncated PIF1 helicases showed no transcriptional activity, with the exception of helicase ID 1079561 (on chromosome X). The HELPO1.1 subfamily displayed very high levels of expression (up to 38.64 RPKM) compared with the HELPO1.3 (maximum of 7.69 RPKM) and HELPO1.2 members (maximum of 2.41 RPKM). RT-qPCR experiments were performed using mRNA from the strains PC9, PC15 and N001 grown in submerged cultures to analyze the expression of the RepHel helicases and captured genes independently. For RepHel helicases, similar relative profiles were observed in the three strains, although the ranges of the transcriptional levels were different (Figure 5F). The RepHel helicase of HELPO1.2 was frequently the most highly expressed (0.31, 20.9 and 6.9 RQs in PC9, PC15 and N001, respectively). HELPO1.1 RepHel showed much lower expression levels (0.25, 1.8 and 0.2 RQs in PC9, PC15 and N001, respectively) and HELPO2 showed no expression in N001 and PC9 (0, 2.6 and 0 RQs in PC9, PC15 and N001, respectively). Virus-like captured genes carried by LTR/Gypsy did not show transcription in any strain, and genes of unknown function, such as capA, capA2, capB and capC, showed a strain-specific expression profile. RT-qPCR experiments performed with PC9 showed that capA was the most highly expressed gene (52.3 RQs) whereas much lower (capB and capC) or no transcription (capA2) was observed for the rest of these genes. In PC15, the highest expression values corresponded to capC and capA2 (30.4 and 22.1 RQs). In N001, capA was the most highly expressed gene, followed by capC and capA2 (8.51, 2.4 and 2.2 RQs) (Figure 5F). Clear differences were observed between the capA and capA2 transcription profiles using RT-qPCR. Because the primers were designed to amplify more than one gene with the exception of capA2, capD and capF (Additional file 6: Table S4), the transcription levels obtained were the result of the contribution of every RepHel helicase and captured gene from each helitron family.Figure 5

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