Irisarri, Iker

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Strassert, Jürgen F. H."],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Williams, Tom A."],["dc.contributor.author","Burki, Fabien"],["dc.date.accessioned","2021-06-01T09:41:39Z"],["dc.date.available","2021-06-01T09:41:39Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth."],["dc.identifier.doi","10.1038/s41467-021-22044-z"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/84995"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.eissn","2041-1723"],["dc.title","A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","105"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Systematic Biology"],["dc.bibliographiccitation.lastpage","120"],["dc.bibliographiccitation.volume","71"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Strassert, Jürgen F H"],["dc.contributor.author","Burki, Fabien"],["dc.contributor.editor","Folk, Ryan"],["dc.date.accessioned","2022-04-01T10:00:31Z"],["dc.date.available","2022-04-01T10:00:31Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and nonmonophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic data sets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual data sets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear data sets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and recovered a putative association with plastid-lacking Picozoa. This study represents an important step toward better understanding deep eukaryotic evolution and the origin of plastids. [Archaeplastida; Bayesian; chloroplast; maximum likelihood; mixture model; ortholog; outlier loci; paralog; protist.]"],["dc.identifier.doi","10.1093/sysbio/syab036"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105450"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.eissn","1076-836X"],["dc.relation.issn","1063-5157"],["dc.title","Phylogenomic Insights into the Origin of Primary Plastids"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1963"],["dc.bibliographiccitation.journal","Proceedings of the Royal Society of London. Series B, Biological Sciences"],["dc.bibliographiccitation.volume","288"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Darienko, Tatyana M."],["dc.contributor.author","Pröschold, Thomas"],["dc.contributor.author","Fürst-Jansen, Janine M. R."],["dc.contributor.author","Jamy, Mahwash"],["dc.contributor.author","de Vries, Jan"],["dc.date.accessioned","2021-12-01T09:21:07Z"],["dc.date.available","2021-12-01T09:21:07Z"],["dc.date.issued","2021"],["dc.description.abstract","Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes."],["dc.description.abstract","Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes."],["dc.identifier.doi","10.1098/rspb.2021.2168"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/94351"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-478"],["dc.relation.eissn","1471-2954"],["dc.relation.issn","0962-8452"],["dc.title","Unexpected cryptic species among streptophyte algae most distant to land plants"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","6348"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Wickell, David"],["dc.contributor.author","Kuo, Li-Yaung"],["dc.contributor.author","Yang, Hsiao-Pei"],["dc.contributor.author","Dhabalia Ashok, Amra"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Dadras, Armin"],["dc.contributor.author","de Vries, Sophie"],["dc.contributor.author","de Vries, Jan"],["dc.contributor.author","Huang, Yao-Moan"],["dc.contributor.author","Li, Zheng"],["dc.contributor.author","Li, Fay-Wei"],["dc.date.accessioned","2021-12-01T09:20:52Z"],["dc.date.available","2021-12-01T09:20:52Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes , an aquatic lycophyte, can also perform CAM as an adaptation to low CO 2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known ‘bacterial-type’ PEPC, along with the ‘plant-type’ exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized."],["dc.description.abstract","Abstract To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes , an aquatic lycophyte, can also perform CAM as an adaptation to low CO 2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known ‘bacterial-type’ PEPC, along with the ‘plant-type’ exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized."],["dc.identifier.doi","10.1038/s41467-021-26644-7"],["dc.identifier.pii","26644"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/94288"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-478"],["dc.relation.eissn","2041-1723"],["dc.title","Underwater CAM photosynthesis elucidated by Isoetes genome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","S1055790321001007"],["dc.bibliographiccitation.firstpage","107167"],["dc.bibliographiccitation.journal","Molecular Phylogenetics and Evolution"],["dc.bibliographiccitation.volume","161"],["dc.contributor.author","Montero-Mendieta, Santiago"],["dc.contributor.author","De la Riva, Ignacio"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Leonard, Jennifer A."],["dc.contributor.author","Webster, Matthew T."],["dc.contributor.author","Vilà, Carles"],["dc.date.accessioned","2021-08-12T07:44:47Z"],["dc.date.available","2021-08-12T07:44:47Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1016/j.ympev.2021.107167"],["dc.identifier.pii","S1055790321001007"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/88295"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-448"],["dc.relation.issn","1055-7903"],["dc.title","Phylogenomics and evolutionary history of Oreobates (Anura: Craugastoridae) Neotropical frogs along elevational gradients"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4473"],["dc.bibliographiccitation.issue","20"],["dc.bibliographiccitation.journal","Current Biology"],["dc.bibliographiccitation.lastpage","4482.e7"],["dc.bibliographiccitation.volume","32"],["dc.contributor.author","Hess, Sebastian"],["dc.contributor.author","Williams, Shelby K."],["dc.contributor.author","Busch, Anna"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Delwiche, Charles F."],["dc.contributor.author","de Vries, Sophie"],["dc.contributor.author","Darienko, Tatyana"],["dc.contributor.author","Roger, Andrew J."],["dc.contributor.author","Archibald, John M."],["dc.contributor.author","Buschmann, Henrik"],["dc.contributor.author","de Vries, Jan"],["dc.date.accessioned","2022-12-01T08:32:00Z"],["dc.date.available","2022-12-01T08:32:00Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1016/j.cub.2022.08.022"],["dc.identifier.pii","S0960982222012994"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/118332"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-621"],["dc.relation.issn","0960-9822"],["dc.rights.uri","https://www.elsevier.com/tdm/userlicense/1.0/"],["dc.title","A phylogenomically informed five-order system for the closest relatives of land plants"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","tpj.15387"],["dc.bibliographiccitation.journal","The Plant Journal"],["dc.contributor.author","de Vries, Sophie"],["dc.contributor.author","Fürst‐Jansen, Janine MR"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Dhabalia Ashok, Amra"],["dc.contributor.author","Ischebeck, Till"],["dc.contributor.author","Feussner, Kirstin"],["dc.contributor.author","Abreu, Ilka N"],["dc.contributor.author","Petersen, Maike"],["dc.contributor.author","Feußner, Ivo"],["dc.contributor.author","de Vries, Jan"],["dc.date.accessioned","2021-07-05T14:57:44Z"],["dc.date.available","2021-07-05T14:57:44Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1111/tpj.15387"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/87724"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-441"],["dc.relation.eissn","1365-313X"],["dc.relation.issn","0960-7412"],["dc.title","The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Seminars in Cell & Developmental Biology"],["dc.contributor.author","Rieseberg, Tim P."],["dc.contributor.author","Dadras, Armin"],["dc.contributor.author","Fürst-Jansen, Janine M.R."],["dc.contributor.author","Dhabalia Ashok, Amra"],["dc.contributor.author","Darienko, Tatyana"],["dc.contributor.author","de Vries, Sophie"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","de Vries, Jan"],["dc.date.accessioned","2022-04-01T10:01:37Z"],["dc.date.available","2022-04-01T10:01:37Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1016/j.semcdb.2022.03.004"],["dc.identifier.pii","S1084952122000738"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105711"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.issn","1084-9521"],["dc.title","Crossroads in the evolution of plant specialized metabolism"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","syac045"],["dc.bibliographiccitation.journal","Systematic Biology"],["dc.contributor.author","Uribe, Juan E"],["dc.contributor.author","González, Vanessa L"],["dc.contributor.author","Irisarri, Iker"],["dc.contributor.author","Kano, Yasunori"],["dc.contributor.author","Herbert, David G"],["dc.contributor.author","Strong, Ellen E"],["dc.contributor.author","Harasewych, M G"],["dc.date.accessioned","2022-07-01T07:35:03Z"],["dc.date.available","2022-07-01T07:35:03Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia."],["dc.identifier.doi","10.1093/sysbio/syac045"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/112076"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-581"],["dc.relation.eissn","1076-836X"],["dc.relation.issn","1063-5157"],["dc.title","A phylogenomic backbone for gastropod molluscs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","nph.18176"],["dc.bibliographiccitation.journal","New Phytologist"],["dc.contributor.author","Fürst‐Jansen, Janine M. R."],["dc.contributor.author","Vries, Sophie"],["dc.contributor.author","Irisarri, Iker"],["dc.date.accessioned","2022-06-01T09:39:31Z"],["dc.date.available","2022-06-01T09:39:31Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1111/nph.18176"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/108497"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-572"],["dc.relation.eissn","1469-8137"],["dc.relation.issn","0028-646X"],["dc.rights.uri","http://creativecommons.org/licenses/by-nc/4.0/"],["dc.title","Different patterns of gene evolution underpin water‐related innovations in land plants"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]