Limits...
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

Phylogenetic reconstruction of the eukaryotic Pif1-like helicase domain. Green represents helitrons from the Plant kingdom, yellow from the Animal kingdom, and blue from the Fungal kingdom. Light blue represents the phylum Basidiomycota and dark blue represents the phylum Ascomycota.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Phylogenetic reconstruction of the eukaryotic Pif1-like helicase domain. Green represents helitrons from the Plant kingdom, yellow from the Animal kingdom, and blue from the Fungal kingdom. Light blue represents the phylum Basidiomycota and dark blue represents the phylum Ascomycota.

Mentions: To investigate the evolutionary relationships of the fungal helitrons identified as well as those from other eukaryotic genomes, we reconstructed molecular phylogenies of the PIF1-like helicase and Helitron helicase-like domains (see Materials and Methods). An initial dataset containing 2175 PIF1-like helicases from 284 fungal genomes (JGI filtered models) and 213 putative autonomous elements obtained from Repbase (including plants, animals and fungi) was used to uncover new insights into the helitron distribution in the eukaryotic domain. A total of 672 sequences bore the PIF1-like helicase domain, 416 carried the Helitron helicase-like domain, and 125 sequences displayed both domains. After removing duplicated copies, the remaining sequences were used for phylogenetic analyses. The functional domains were extracted from the sequences and aligned using custom Python scripts. Both analyses (Figure 6 and Additional file 7: Figure S2) depicted a similar scenario - fungal helitrons were not monophyletic, but rather they appeared in at least four different clades interspersed among metazoan and plant helitrons. In addition, within each fungal clade, the different fungal phyla (e.g., ascomycetes, basidiomycetes) appeared mixed.Figure 6


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)

Phylogenetic reconstruction of the eukaryotic Pif1-like helicase domain. Green represents helitrons from the Plant kingdom, yellow from the Animal kingdom, and blue from the Fungal kingdom. Light blue represents the phylum Basidiomycota and dark blue represents the phylum Ascomycota.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Phylogenetic reconstruction of the eukaryotic Pif1-like helicase domain. Green represents helitrons from the Plant kingdom, yellow from the Animal kingdom, and blue from the Fungal kingdom. Light blue represents the phylum Basidiomycota and dark blue represents the phylum Ascomycota.
Mentions: To investigate the evolutionary relationships of the fungal helitrons identified as well as those from other eukaryotic genomes, we reconstructed molecular phylogenies of the PIF1-like helicase and Helitron helicase-like domains (see Materials and Methods). An initial dataset containing 2175 PIF1-like helicases from 284 fungal genomes (JGI filtered models) and 213 putative autonomous elements obtained from Repbase (including plants, animals and fungi) was used to uncover new insights into the helitron distribution in the eukaryotic domain. A total of 672 sequences bore the PIF1-like helicase domain, 416 carried the Helitron helicase-like domain, and 125 sequences displayed both domains. After removing duplicated copies, the remaining sequences were used for phylogenetic analyses. The functional domains were extracted from the sequences and aligned using custom Python scripts. Both analyses (Figure 6 and Additional file 7: Figure S2) depicted a similar scenario - fungal helitrons were not monophyletic, but rather they appeared in at least four different clades interspersed among metazoan and plant helitrons. In addition, within each fungal clade, the different fungal phyla (e.g., ascomycetes, basidiomycetes) appeared mixed.Figure 6

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