Non-photosynthetic predators are sister to red algae

Gawryluk, Ryan M.R.; Tikhonenkov, Denis V.; Hehenberger, Elisabeth; Husník, Filip; Mylnikov, Alexander P.; Keeling, Patrick J.

doi:10.1038/s41586-019-1398-6

Cited by 124 publications

(185 citation statements)

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“…are correct)? The serendipitous discovery of cryptic algal lineages with a close relationship to land plants would help (in effect, a discovery parallel to the recent identification of a close non‐photosynthetic sister group to red algae; Gawryluk et al., ). In the absence of such good luck, improved substitutional models may help, as would the discovery of rare genomic or morphological changes that unambiguously support one or another resolution of early land‐plant relationships.…”

Section: Discussionmentioning

confidence: 99%

Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution

Bell

Lin

Gerelle

et al. 2019

American J of Botany

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PREMISE: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS:We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS:Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS:A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure. , et al. 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. APPENDIX S6. Circular plastome map of Buxbaumia aphylla. APPENDIX S7. Circular plastome map of Diphyscium foliosum. APPENDIX S8. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the unpartitioned plastid nucleotide analysis, with likelihood bootstrap support values indicated above branches. APPENDIX S9. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the gene-by-codon partitioned plastid nucleotide analysis, with likelihood bootstrap support values indicated above branches.APPENDIX S10. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the unpartitioned plastid amino-acid analysis, with likelihood bootstrap support values indicated above branches. APPENDIX S11. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the gene-partitioned plastid amino-acid analysis, with likeli...

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Section: Discussionmentioning

confidence: 99%

Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution

Bell

Lin

Gerelle

et al. 2019

American J of Botany

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“…A large number of extant microbial eukaryotes have never been examined using transcriptomic or genomic techniques, and some of them may hold the keys to resolving important unanswered questions in eukaryotic phylogeny and evolution. Thus, to reconstruct the evolutionary relationships among the major eukaryotic assemblages to a resolution that is both accurate and informative, the taxon sampling in phylogenomic analyses has been improved by targeting two classes of organisms: (i) Novel microbial eukaryotes that represent lineages that were previously unknown to science, and (ii) “orphan eukaryotes” that had been reported before, but whose evolutionary affiliations were unresolved by morphological examinations and/or single-gene phylogenies (Zhao et al 2012; Kamikawa et al 2014; Yabuki et al 2014; Burki et al 2016; Janouškovec et al 2017; Brown et al 2018; Lax et al 2018; Gawryluk et al 2019; Strassert et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related organelles generating no ATP

Yazaki

Kume

Shiratori

et al. 2019

Preprint

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23Running head: Phylogeny and putative MRO functions in a new metamonad clade. 25Abstract 28 We here report the phylogenetic position of barthelonids, small anaerobic flagellates 29 previously examined using light microscopy alone. Barthelona spp. were isolated from 30 geographically distinct regions and we established five laboratory strains. Transcriptomic data 31 generated from one Barthelona strain (PAP020) was used for large-scale, multi-gene 32 phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the 33 base of the Fornicata clade, indicating that barthelonids represent a deep-branching 34 Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and 35 preliminary electron microscopy observations on strain PAP020, we suspected that 36 barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-37 related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 38 were predicted based on its transcriptomic data and compared with those in the MROs of 39 fornicates. Strain PAP020 is most likely incapable of generating ATP in the MRO, as no 40 mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. 41 Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), 42 suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two 43 separate losses of substrate-level phosphorylation from the MRO in the clade containing 44 barthelonids and (other) fornicates.45 46

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“…An analogous example is the recent finding of Rhodelphis; gene and intron rich, phagotrophic flagellates that contain a genome‐lacking primary plastid and form a sister group to red algae (Rhodophyta) within the Archaeplastida (Gawryluk et al. ). This novel heterotrophic lineage would not in any sensible taxonomic scheme be considered as heterotrophic Rhodophyta because they lack the major attributes of red algae, namely, highly reduced nuclear gene inventories with few introns, lack of phagotrophy, absence of flagella and basal bodies, and a phycobilisome‐containing photosynthetic organelle (Bhattacharya et al.…”

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confidence: 91%