Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin

Handle URI:
http://hdl.handle.net/10754/325443
Title:
Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin
Authors:
Burki, Fabien; Flegontov, Pavel; Oborník, Miroslav; Cihlář, Jaromír; Pain, Arnab ( 0000-0002-1755-2819 ) ; Lukeš, Julius; Keeling, Patrick J.
Abstract:
The transition from endosymbiont to organelle in eukaryotic cells involves the transfer of significant numbers of genes to the host genomes, a process known as endosymbiotic gene transfer (EGT). In the case of plastid organelles, EGTs have been shown to leave a footprint in the nuclear genome that can be indicative of ancient photosynthetic activity in present-day plastid-lacking organisms, or even hint at the existence of cryptic plastids. Here,we evaluated the impact of EGTon eukaryote genomes by reanalyzing the recently published EST dataset for Chromera velia, an interesting test case of a photosynthetic alga closely related to apicomplexan parasites. Previously, 513 genes were reported to originate from red and green algae in a 1:1 ratio. In contrast, by manually inspecting newly generated trees indicating putative algal ancestry, we recovered only 51 genes congruent with EGT, of which 23 and 9 were of red and green algal origin, respectively,whereas 19 were ambiguous regarding the algal provenance.Our approach also uncovered 109 genes that branched within a monocot angiosperm clade, most likely representing a contamination. We emphasize the lack of congruence and the subjectivity resulting from independent phylogenomic screens for EGT, which appear to call for extreme caution when drawing conclusions for major evolutionary events. 2012 The Author(s).
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Burki F, Flegontov P, Obornik M, Cihlar J, Pain A, et al. (2012) Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin. Genome Biology and Evolution 4: evs049-evs049. doi:10.1093/gbe/evs049.
Publisher:
Oxford University Press (OUP)
Journal:
Genome Biology and Evolution
Issue Date:
16-May-2012
DOI:
10.1093/gbe/evs049
PubMed ID:
22593553
PubMed Central ID:
PMC3516247
Type:
Article
ISSN:
17596653
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBurki, Fabienen
dc.contributor.authorFlegontov, Pavelen
dc.contributor.authorOborník, Miroslaven
dc.contributor.authorCihlář, Jaromíren
dc.contributor.authorPain, Arnaben
dc.contributor.authorLukeš, Juliusen
dc.contributor.authorKeeling, Patrick J.en
dc.date.accessioned2014-08-27T09:51:33Z-
dc.date.available2014-08-27T09:51:33Z-
dc.date.issued2012-05-16en
dc.identifier.citationBurki F, Flegontov P, Obornik M, Cihlar J, Pain A, et al. (2012) Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin. Genome Biology and Evolution 4: evs049-evs049. doi:10.1093/gbe/evs049.en
dc.identifier.issn17596653en
dc.identifier.pmid22593553en
dc.identifier.doi10.1093/gbe/evs049en
dc.identifier.urihttp://hdl.handle.net/10754/325443en
dc.description.abstractThe transition from endosymbiont to organelle in eukaryotic cells involves the transfer of significant numbers of genes to the host genomes, a process known as endosymbiotic gene transfer (EGT). In the case of plastid organelles, EGTs have been shown to leave a footprint in the nuclear genome that can be indicative of ancient photosynthetic activity in present-day plastid-lacking organisms, or even hint at the existence of cryptic plastids. Here,we evaluated the impact of EGTon eukaryote genomes by reanalyzing the recently published EST dataset for Chromera velia, an interesting test case of a photosynthetic alga closely related to apicomplexan parasites. Previously, 513 genes were reported to originate from red and green algae in a 1:1 ratio. In contrast, by manually inspecting newly generated trees indicating putative algal ancestry, we recovered only 51 genes congruent with EGT, of which 23 and 9 were of red and green algal origin, respectively,whereas 19 were ambiguous regarding the algal provenance.Our approach also uncovered 109 genes that branched within a monocot angiosperm clade, most likely representing a contamination. We emphasize the lack of congruence and the subjectivity resulting from independent phylogenomic screens for EGT, which appear to call for extreme caution when drawing conclusions for major evolutionary events. 2012 The Author(s).en
dc.language.isoenen
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0en
dc.subjectAlgaeen
dc.subjectChromeraen
dc.subjectEndosymbiotic gene transferen
dc.subjectPlastid evolutionen
dc.subjectProtisten
dc.subjectalgaeen
dc.subjectApicomplexaen
dc.subjectChlorophytaen
dc.subjectEukaryotaen
dc.subjectMagnoliophytaen
dc.subjectProtistaen
dc.subjectAlveolataen
dc.subjectclassificationen
dc.subjectcytologyen
dc.subjectgeneticsen
dc.subjectgreen algaen
dc.subjecthorizontal gene transferen
dc.subjectmolecular evolutionen
dc.subjectphylogenyen
dc.subjectphysiologyen
dc.subjectplastiden
dc.subjectred algaen
dc.subjectsymbiosisen
dc.subjectAlveolataen
dc.subjectChlorophytaen
dc.subjectEvolution, Molecularen
dc.subjectGene Transfer, Horizontalen
dc.subjectPhylogenyen
dc.subjectPlastidsen
dc.subjectRhodophytaen
dc.subjectSymbiosisen
dc.titleRe-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal originen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGenome Biology and Evolutionen
dc.identifier.pmcidPMC3516247en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCanadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canadaen
dc.contributor.institutionBiology Centre, Institute of Parasitology, Czech Academy of Sciences, ?esk Bud?jovice, Czech Republicen
dc.contributor.institutionFaculty of Science, University of South Bohemia, ?esk Bud?jovice, Czech Republicen
dc.contributor.institutionInstitute of Microbiology, Czech Academy of Sciences, T?ebo?, Czech Republicen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

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