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A single loss of photosynthesis in diatoms

https://doi.org/10.1101/298810
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Photosynthetic evolution in parasitic plants: insight from the chloroplast genome
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Red algal parasites: Models for a life history evolution that leaves photosynthesis behind again and again
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Plastid translation and transcription genes in a non‐photosynthetic plant: intact, missing and pseudo genes.
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Differential heterotrophic utilization of organic compounds by diatoms and bacteria under light and dark conditions
inferredcites →https://doi.org/10.1007/978-1-4615-5419-6_8openalex-snapshot
Molecular Phylogenetic and Evolutionary Studies of Parasitic Plants
inferredcites →https://doi.org/10.1007/bf00161168openalex-snapshot
Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: Loss or accelerated sequence evolution of tRNA and ribosomal protein genes
inferredcites →https://doi.org/10.1007/bf00175504openalex-snapshot
Chloroplast DNA codon use: Evidence for selection at the psb A locus based on tRNA availability
inferredcites →https://doi.org/10.1007/bf00455920openalex-snapshot
Role of silicon in diatom metabolism
inferredcites →https://doi.org/10.1007/bf02352296openalex-snapshot
Selection on the codon bias ofChlamydomonas reinhardtii chloroplast genes and the plantpsbA gene
inferredcites →https://doi.org/10.1007/pl00006325openalex-snapshot
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages
inferredcites →https://doi.org/10.1007/s00239-004-0353-8openalex-snapshot
Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)
inferredcites →https://doi.org/10.1007/s002390010210openalex-snapshot
Dinoflagellate Nuclear SSU rRNA Phylogeny Suggests Multiple Plastid Losses and Replacements
inferredcites →https://doi.org/10.1007/s002399910020openalex-snapshot
Codon Usage in Plastid Genes Is Correlated with Context, Position Within the Gene, and Amino Acid Content
inferredcites →https://doi.org/10.1007/s00294-008-0208-8openalex-snapshot
From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants
inferredcites →https://doi.org/10.1007/s00294-017-0761-0openalex-snapshot
Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists
inferredcites →https://doi.org/10.1007/s00438-002-0681-6openalex-snapshot
The genes encoding subunits of ATP synthase are conserved in the reduced plastid genome of the heterotrophic alga Prototheca wickerhamii
inferredcites →https://doi.org/10.1007/s10265-010-0395-5openalex-snapshot
Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms
inferredcites →https://doi.org/10.1007/s10750-005-1612-4openalex-snapshot
Differential Heterotrophic Utilization of Organic Compounds by Diatoms and Bacteria under Light and Dark Conditions
inferredcites →https://doi.org/10.1016/bs.abr.2017.11.009openalex-snapshot
Evolution of the Plastid Genomes in Diatoms
inferredcites →https://doi.org/10.1016/j.algal.2012.04.003openalex-snapshot
Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways
inferredcites →https://doi.org/10.1016/j.cub.2008.05.042openalex-snapshot
Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic
inferredcites →https://doi.org/10.1016/j.cub.2008.11.067openalex-snapshot
The Puzzle of Plastid Evolution
inferredcites →https://doi.org/10.1016/j.ecss.2009.07.012openalex-snapshot
First account of apochlorotic diatoms from intertidal sand of a south Florida beach
inferredcites →https://doi.org/10.1016/j.femsle.2004.02.006openalex-snapshot
The non-photosynthetic, pathogenic green algaHelicosporidiumsp. has retained a modified, functional plastid genome
inferredcites →https://doi.org/10.1016/j.hal.2013.12.004openalex-snapshot
Morphology and molecular phylogeny of Nitzschia bizertensis sp. nov.—A new domoic acid-producer
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Why are plastid genomes retained in non-photosynthetic organisms?
inferredcites →https://doi.org/10.1016/j.ympev.2007.03.024openalex-snapshot
Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
inferredcites →https://doi.org/10.1017/s0269-915x(05)00304-6openalex-snapshot
Plants parasitic on fungi: unearthing the fungi in myco-heterotrophs and debunking the ‘saprophytic’ plant myth
inferredcites →https://doi.org/10.1017/s0269915x05003046openalex-snapshot
Plants parasitic on fungi: unearthing the fungi in myco-heterotrophs and debunking the plant myth
inferredcites →https://doi.org/10.1017/s096702620100347xopenalex-snapshot
Phylogeny of the Bacillariaceae with emphasis on the genusPseudo-nitzschia(Bacillariophyceae) based on partial LSU rDNA
inferredcites →https://doi.org/10.1038/178480a0openalex-snapshot
Micro-Organisms from Decaying Seaweed
inferredcites →https://doi.org/10.1038/364440a0openalex-snapshot
Confidence in evolutionary trees from biological sequence data
inferredcites →https://doi.org/10.1038/380398a0openalex-snapshot
Human parasite finds taxonomic home
inferredcites →https://doi.org/10.1038/381482a0openalex-snapshot
Plastid in human parasites
inferredcites →https://doi.org/10.1038/nature20803openalex-snapshot
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus
inferredcites →https://doi.org/10.1038/srep14465openalex-snapshot
Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae
inferredcites →https://doi.org/10.1046/j.1529-8817.1999.00001-137.xopenalex-snapshot
PLASTID FATTY ACID BIOSYNTHESIS IN THE DIATOMS NITZSCHIA ALBA AND NITZSCHIA LAEVIS
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The reversible effect of flow on the morphology of ceratocorys horrida (PERIDINIALES, DINOPHYTA)*
inferredcites →https://doi.org/10.1073/pnas.1607576113openalex-snapshot
Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants
inferredcites →https://doi.org/10.1073/pnas.92.24.11317openalex-snapshot
Inferring phylogenies from DNA sequences of unequal base compositions.
inferredcites →https://doi.org/10.1073/pnas.95.21.12352openalex-snapshot
Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum
inferredcites →https://doi.org/10.1078/1434461000159openalex-snapshot
Origin and Fate of Chloroplasts in the Euglenoida
inferredcites →https://doi.org/10.1078/s1434-4610(04)70033-4openalex-snapshot
Complete Gene Map of the Plastid Genome of the Nonphotosynthetic Euglenoid Flagellate Astasia longa
inferredcites →https://doi.org/10.1080/0269249x.2011.597988openalex-snapshot
Molecular phylogeny of the family Bacillariaceae based on 18S rDNA sequences: focus on freshwaterNitzschiaof the sectionLanceolatae
inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferredcites →https://doi.org/10.1093/bioinformatics/bth352openalex-snapshot
Automatic annotation of organellar genomes with DOGMA
inferredcites →https://doi.org/10.1093/bioinformatics/btp157openalex-snapshot
Infernal 1.0: inference of RNA alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btr039openalex-snapshot
Easyfig: a genome comparison visualizer
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/gbe/evp047openalex-snapshot
The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate
inferredcites →https://doi.org/10.1093/gbe/evu039openalex-snapshot
Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msv134openalex-snapshot
Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes
inferredcites →https://doi.org/10.1093/molbev/msx172openalex-snapshot
A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in Plastids
inferredcites →https://doi.org/10.1093/molbev/msx268openalex-snapshot
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)
inferredcites →https://doi.org/10.1093/nar/gkh152openalex-snapshot
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
inferredcites →https://doi.org/10.1093/sysbio/syu070openalex-snapshot
The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters
inferredcites →https://doi.org/10.1098/rstb.2009.0103openalex-snapshot
The endosymbiotic origin, diversification and fate of plastids
inferredcites →https://doi.org/10.1099/00221287-46-3-361openalex-snapshot
Culture and Nutrition of Some Apochlorotic Diatoms of the Genus Nitzschia
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EVOLUTIONARY CONSEQUENCES OF THE LOSS OF PHOTOSYNTHESIS IN CHLAMYDOMONADACEAE: PHYLOGENETIC ANALYSIS OFRrn18(18S rDNA) IN 13POLYTOMASTRAINS (CHLOROPHYTA)1
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THE EVOLUTION OF PARASITISM IN THE RED ALGAE: MOLECULAR COMPARISONS OF ADELPHOPARASITES AND THEIR HOSTS1
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MOLECULAR PHYLOGENY AND EVOLUTION OF RED ALGAL PARASITES: A CASE STUDY OF BENZAITENIA, JANCZEWSKIA, AND ULULANIA (CERAMIALES)1
inferredcites →https://doi.org/10.1111/j.1550-7408.1960.tb00740.xopenalex-snapshot
A Mutant of Chlamydomonas moewusii lacking contractile vacuoles*
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Principles of Protein and Lipid Targeting in Secondary Symbiogenesis: Euglenoid, Dinoflagellate, and Sporozoan Plastid Origins and the Eukaryote Family Tree 1 , 2
inferredcites →https://doi.org/10.1111/j.1550-7408.2002.tb00336.xopenalex-snapshot
Re‐examining Alveolate Evolution Using Multiple Protein Molecular Phylogenies
inferredcites →https://doi.org/10.1111/j.1550-7408.2008.00388.xopenalex-snapshot
First Account of Apochlorotic Diatoms from Mangrove Waters in Florida
inferredcites →https://doi.org/10.1111/j.1550-7408.2009.00449.xopenalex-snapshot
Morphology, Ultrastructure, and Small Subunit rDNA Phylogeny of the Marine Heterotrophic Flagellate Goniomonas aff. amphinema
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00349.xopenalex-snapshot
FINE-SCALE PHYLOGEOGRAPHIC CONGRUENCE DESPITE DEMOGRAPHIC INCONGRUENCE IN TWO LOW-MOBILITY SAPROXYLIC SPRINGTAILS
inferredcites →https://doi.org/10.1111/nph.13279openalex-snapshot
When the lights go out: the evolutionary fate of free‐living colorless green algae
inferredcites →https://doi.org/10.1111/nph.14557openalex-snapshot
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom
inferredcites →https://doi.org/10.1111/pre.12072openalex-snapshot
Multiple losses of photosynthesis in N itzschia ( B acillariophyceae)
inferredcites →https://doi.org/10.1126/science.1128796openalex-snapshot
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
inferredcites →https://doi.org/10.1126/science.281.5374.237openalex-snapshot
Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components
inferredcites →https://doi.org/10.1127/pip/2015/0027openalex-snapshot
Red algae provide fertile ground for exploring parasite evolution
inferredcites →https://doi.org/10.1128/ec.4.2.253-261.2005openalex-snapshot
Multiple Metabolic Roles for the Nonphotosynthetic Plastid of the Green Alga Prototheca wickerhamii
inferredcites →https://doi.org/10.1146/annurev.arplant.51.1.111openalex-snapshot
N ONPHOTOSYNTHETIC M ETABOLISM IN P LASTIDS
inferredcites →https://doi.org/10.1163/ej.9789004167506.i-438openalex-snapshot
Parasitic flowering plants
inferredcites →https://doi.org/10.1177/03635465980260041401openalex-snapshot
The Effects of Platelet-Derived Growth Factor-BB on Healing of the Rabbit Medial Collateral Ligament
inferredcites →https://doi.org/10.1186/1471-2105-3-2openalex-snapshot
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
inferredcites →https://doi.org/10.1186/1471-2148-13-126openalex-snapshot
Parasitic plants have increased rates of molecular evolution across all three genomes
inferredcites →https://doi.org/10.1186/1471-2148-5-16openalex-snapshot
Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function
inferredcites →https://doi.org/10.1186/1471-2148-7-248openalex-snapshot
Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2012-13-12-r122openalex-snapshot
Ray Meta: scalable de novo metagenome assembly and profiling
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Unravelling the algae
inferredcites →https://doi.org/10.21775/cimb.007.057openalex-snapshot
The Apicoplast: A Review of the Derived Plastid of Apicomplexan Parasites
inferredcites →https://doi.org/10.2216/14-002.1openalex-snapshot
Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites
inferredcites →https://doi.org/10.2216/i0031-8884-32-3-234.1openalex-snapshot
Stichochrysis immobilis is a diatom, not a chrysophyte
inferredcites →https://doi.org/10.2216/i0031-8884-38-6-437.1openalex-snapshot
The species concept in diatoms
inferredcites →https://doi.org/10.4319/lo.1997.42.1.0198openalex-snapshot
Phagotrophy in phototrophs
inferredcites →https://doi.org/10.5091/plecevo.2016.1097openalex-snapshot
Functional biology of parasitic plants: a review
inferredcites →https://doi.org/10.5586/asbp.2014.047openalex-snapshot
Are all red algal parasites cut from the same cloth?

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.gde.2019.07.013openalex-snapshot
Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles
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