Protist evolution and biology
484 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Scooped by Anders Kristian Krabberød
Scoop.it!

A Eukaryote without a Mitochondrial Organelle

A Eukaryote without a Mitochondrial Organelle | Protist evolution and biology | Scoop.it
Anna Karnkowska, Vojtěch Vacek, Zuzana Zubáčová, Sebastian C. Treitli, Romana Petrželková, Laura Eme, Lukáš Novák, Vojtěch Žárský, Lael D. Barlow, Emily K. Herman, Petr Soukal, Miluše Hroudová, Pavel Doležal, Courtney W. Stairs, Andrew J. Roger, Marek Eliáš, Joel B. Dacks, Čestmír Vlček, Vladimír Hampl

Highlights 
•Monocercomonoides sp. is a eukaryotic microorganism with no mitochondria 
•The complete absence of mitochondria is a secondary loss, not an ancestral feature 
•The essential mitochondrial ISC pathway was replaced by a bacterial SUF system 

Summary: The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondrial iron-sulfur cluster assembly pathway, thought to be conserved in virtually all eukaryotic cells, has been replaced by a cytosolic sulfur mobilization system (SUF) acquired by lateral gene transfer from bacteria. In the context of eukaryotic phylogeny, our data suggest that Monocercomonoides is not primitively amitochondrial but has lost the mitochondrion secondarily. This is the first example of a eukaryote lacking any form of a mitochondrion, demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. | Protist evolution and biology | Scoop.it
The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Ecological impacts of parasitic chytrids, syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates

Ecological impacts of parasitic chytrids, syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates | Protist evolution and biology | Scoop.it

Publication date: February 2016
Source:Fungal Ecology, Volume 19
Author(s): Thomas G. Jephcott, Catharina Alves-de-Souza, Frank H. Gleason, Floris F. van Ogtrop, Télesphore Sime-Ngando, Sergey A.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria)

Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria) | Protist evolution and biology | Scoop.it

Publication date: July 2015 Source:Protist, Volume 166, Issue 3 Author(s): Tristan Biard, Loïc Pillet, Johan Decelle, Camille Poirier, Noritoshi Suzuki, Fabrice Not 

 

Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists. They occur as either large colonies or solitary specimens, and, unlike most radiolarians, some taxa lack silicified structures. Collodarians are known to play an important role in oceanic food webs as both active predators and hosts of symbiotic microalgae, yet very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Here we investigated collodarian diversity using phylogenetic analyses of both nuclear small (18S) and large (28S) subunits of the ribosomal DNA, including 124 new sequences from 75 collodarians sampled worldwide. The resulting molecular phylogeny was compared to morphology-based classification. Our analyses distinguished the monophyletic clade of skeleton-less and spicule-bearing Sphaerozoidae from the sister clades Collosphaeridae (skeleton-bearing) and Collophidiidae (skeleton-less), while the Thalassicollidae was not retrieved as a monophyletic clade. Detailed morphological examination with electron microscopy combined with molecular analyses revealed many discrepancies, such as a mix between solitary and colonial species, co-existence of skeleton-less and skeleton-bearing specimens within the Collosphaeridae, as well as complex intraspecific variability in silicified structures. Such observations challenge a morphology-based classification and highlight the pertinence of an integrative taxonomic approach to study collodarian diversity.

 
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats

Publication date: September 2015
Source:Protist, Volume 166, Issue 4
Author(s): Jong Soo Park, Alastair G.B.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Molecular Phylogeny and Morphology of Leannia veloxifera n. gen. et sp. Unveils a New Lineage of Monothalamous Foraminifera - Apothéloz-Perret-Gentil - 2014 - Journal of Eukaryotic Microbiology - W...

Molecular Phylogeny and Morphology of Leannia veloxifera n. gen. et sp. Unveils a New Lineage of Monothalamous Foraminifera - Apothéloz-Perret-Gentil - 2014 - Journal of Eukaryotic Microbiology - W... | Protist evolution and biology | Scoop.it

RT @animalculum: Leannia veloxifera - New Lineage of Monothalamous Foraminifera #protists.

http://t.co/UhRJY957i6 http://t.co/ve6vArep6q

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Single-Cell Sequencing Technologies: Current and Future

Abstract

Intensively developed in the last few years, single-cell sequencing technologies now present numerous advantages over traditional sequencing methods for solving the problems of biological heterogeneity and low quantities of available biological materials. The application of single-cell sequencing technologies has profoundly changed our understanding of a series of biological phenomena, including gene transcription, embryo development, and carcinogenesis. However, before single-cell sequencing technologies can be used extensively, researchers face the serious challenge of overcoming inherent issues of high amplification bias, low accuracy and reproducibility. Here, we simply summarize the techniques used for single-cell isolation, and review the current technologies used in single-cell genomic, transcriptomic, and epigenomic sequencing. We discuss the merits, defects, and scope of application of single-cell sequencing technologies and then speculate on the direction of future developments.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing | Protist evolution and biology | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Response of the protozooplankton assemblage during the European Iron Fertilization Experiment (EIFEX) in the Antarctic circumpolar current

Response of the protozooplankton assemblage during the European Iron Fertilization Experiment (EIFEX) in the Antarctic circumpolar current | Protist evolution and biology | Scoop.it

Ocean iron fertilization experiments enable the quantitative study of processes shaping the structure and functioning of pelagic ecosystems following perturbation under in situ conditions. EIFEX was conducted within a stationary eddy adjacent to the Antarctic Polar Front over 38 days in February/March 2004 and induced a massive diatom bloom. Here, we present the responses in abundance and biomass of all identifiable protozooplankton taxa (heterotrophic protists ranging from 2 to 500 µm) during the bloom. Acantharia, dinoflagellates and ciliates together contributed >90% of protozooplankton biomass in the upper 100 m throughout the experiment with heterotrophic nanoflagellates, nassellaria, spumellaria, phaeodaria, foraminifera and the taxopodidean Sticholonche zanclea providing the remainder. Total protozooplankton biomass increased slightly from 1.0 to 1.3 g C m−2 within the fertilized patch and remained at 0.7+0.04 g C m−2 outside it. However, distinct trends in population build-up or decline were observed within the dominant taxa in each group. In general, smaller less-defended groups such as aloricate ciliates and athecate dinoflagellates declined, whereas the biomass of large, spiny and armoured groups, in particular acantharia, large tintinnids and thecate dinoflagellates increased inside the patch. We attribute the higher accumulation rates of defended taxa to selective, heavy grazing pressure by the large stocks of copepods. Of the defended taxa, acantharia had the lowest mortality rates and the highest biomass. Large stocks of tintinnid loricae in the deep water column identify this group as a relevant contributor to deep organic carbon export. Highest accumulation rates (0.11 day−1) were recorded in S. zanclea.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Uncovering sibling species in Radiolaria: Evidence for ecological partitioning in a marine planktonic protist

Uncovering sibling species in Radiolaria: Evidence for ecological partitioning in a marine planktonic protist | Protist evolution and biology | Scoop.it

Phylogeography of unicellular plankton, as representative pelagic organisms, is fundamental to understanding their evolution in the ocean. Historically, these microplankton were believed to have cosmopolitan distributions achieved through passive transport and little potential for speciation because of a lack of geographic barriers in the oceans. Recent phylogeographic studies of these microplankton, however, have often revealed high diversity and fine-scale geographic distributions. These apparent contradictions may result from poor knowledge of the spatial distributions of pelagic microplankton in the water column. More information about both geographic and vertical distributions of pelagic populations could reveal the dispersal pathways, gene flow, and resulting diversifications in the open ocean. Here we demonstrate that two genetic types of the radiolarian morphospecies Spongotrochus glacialis with morphological differences are vertically segregated into the upper and lower surface waters within the pycnocline of the North Pacific Subtropical Water. This vertically separated distribution of two sister species is associated with distinct ecological partitioning. These two species could survive on different food resources from their respective environments: one in oligotrophic surface waters by using nutrients from symbionts, and the other at greater depths by depending on both heterotrophic and symbiotic nutrition. Moreover, molecular divergence-time estimates suggest that the two species diverged during the period of oligotrophic surface-water development in the Pacific Ocean. Our findings suggest that genetic isolation in the vertical dimension occurs through ecological partitioning even in the absence of physical barriers in the pelagic oceans.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca

Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca | Protist evolution and biology | Scoop.it

We describe 11 new species of Thaumatomonadida using light and electron microscopy and rDNA gene sequences (18S, ITS1, 5.8S, ITS2). We found clear distinctions between major clades in molecular and morphological traits that support now splitting Thaumatomastix into three genera: new marine generaOvaloplaca (oval plate-scales) and Thaumatospina (triangular plate-scales), both with distinctive radially-symmetric bobbin-based spine-scales, restricting Thaumatomastix to freshwater species with putatively non-homologous eccentric-spine scales and thicker triangular plate-scales. New genus Scutellomonas lacks spine-scales, having oval plate-scales with deeply-dished upper tier as in Ovaloplaca, with which it forms a clade having short/absent anterior cilium. Cowlomonas gen. n. is possibly naked. We describe two new Allasspecies, two new Thaumatomonas, and one new Reckertia species, and transfer R. hindoni toThaumatomonas. Triangular-scaled Reckertia has varied plate-scales and ciliary scales. ThaumatomonasrDNA trees reveal two clades: zhukovi/seravini (predominantly triangular scales);coloniensis/oxoniensis/lauterborni/constricta/solis (scales mostly oval). We hypothesise that the ancestor of Thaumatomonadidae had radially-symmetric bobbin-based spine-scales and triangular plate-scales, bobbin-based spine-scales being lost in one lineage and eccentric-spine scales evolving in Thaumatomastix. Bobbin-based spine-scales arguably evolved from triangular plate-scales and single-tier ciliary scales (Ovaloplaca and Reckertia only) from plate-scale rudiments. We present a unified scheme for scale evolution and development in Imbricatea.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages | Protist evolution and biology | Scoop.it

The Ciliophora is one of the most studied protist lineages because of its important ecological role in the microbial loop. While there is an abundance of molecular data for many ciliate groups, it is commonly limited to the 18S ribosomal RNA locus. There is a paucity of data when it comes to availability of protein-coding genes especially for taxa that do not belong to the class Oligohymenophorea. To address this gap, we have sequenced EST libraries for 11 ciliate species. A supermatrix was constructed for phylogenomic analysis based on 158 genes and 42,158 characters and included 16 ciliates, four dinoflagellates and nine apicomplexans. This is the first multigene-based analysis focusing on the phylum Ciliophora. Our analyses reveal two robust superclades within the Intramacronucleata; one composed of the classes Spirotrichea, Armophorea and Litostomatea (SAL) and another with Colpodea and Oligohymenophorea. Furthermore, we provide corroborative evidence for removing the ambiguous taxon Protocruzia from the class Spirotrichea and placing it as incertae sedis in the phylum Ciliophora.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Environmental Breviatea harbour mutualistic Arcobacter epibionts

Environmental Breviatea harbour mutualistic Arcobacter epibionts | Protist evolution and biology | Scoop.it
Emmo Hamann, Harald Gruber-Vodicka, Manuel Kleiner, Halina E. Tegetmeyer, Dietmar Riedel, Sten Littmann, Jianwei Chen, Jana Milucka, Bernhard Viehweger, Kevin W. Becker, Xiaoli Dong, Courtney W. Stairs, Kai-Uwe Hinrichs, Matthew W. Brown, Andrew J. Roger & Marc Strous

Breviatea form a lineage of free living, unicellular protists, distantly related to animals and fungi1, 2. This lineage emerged almost one billion years ago, when the oceanic oxygen content was low, and extant Breviatea have evolved or retained an anaerobic lifestyle3, 4. Here we report the cultivation of Lenisia limosa, gen. et sp. nov., a newly discovered breviate colonized by relatives of animal-associated Arcobacter. Physiological experiments show that the association of L. limosa with Arcobacter is driven by the transfer of hydrogen and is mutualistic, providing benefits to both partners. With whole-genome sequencing and differential proteomics, we show that an experimentally observed fitness gain of L. limosa could be explained by the activity of a so far unknown type of NAD(P)H-accepting hydrogenase, which is expressed in the presence, but not in the absence, of Arcobacter. Differential proteomics further reveal that the presence of Lenisia stimulates expression of known ‘virulence’ factors by Arcobacter. These proteins typically enable colonization of animal cells during infection5, but may in the present case act for mutual benefit. Finally, re-investigation of two currently available transcriptomic data sets of other Breviatea4 reveals the presence and activity of related hydrogen-consuming Arcobacter, indicating that mutualistic interaction between these two groups of microbes might be pervasive. Our results support the notion that molecular mechanisms involved in virulence can also support mutualism6, as shown here for Arcobacter and Breviatea.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits - Annual Review of Microbiology, 70(1):

Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits - Annual Review of Microbiology, 70(1): | Protist evolution and biology | Scoop.it
The DNA double helix has been called one of life’s most elegant structures, largely because of its universality, simplicity, and symmetry. The expression of information encoded within DNA, however, can be far from simple or symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukaryotes). The nuclear and organelle genomes of protists are subject to the most tangled forms of gene expression yet identified. The complicated and extravagant picture of the underlying genetics of eukaryotic microbial life changes how we think about the flow of genetic information and the evolutionary processes shaping it. Here, we discuss the origins, diversity, and growing interest in noncanonical protist gene expression and its relationship to genomic architecture.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp

The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp | Protist evolution and biology | Scoop.it
Background
The protist Plasmodiophora brassicae is a soil-borne pathogen of cruciferous species and the causal agent of clubroot disease of Brassicas including agriculturally important crops such as canola/rapeseed (Brassica napus). P. brassicae has remained an enigmatic plant pathogen and is a rare example of an obligate biotroph that resides entirely inside the host plant cell. The pathogen is the cause of severe yield losses and can render infested fields unsuitable for Brassica crop growth due to the persistence of resting spores in the soil for up to 20 years.
Results To provide insight into the biology of the pathogen and its interaction with its primary host B. napus, we produced a draft genome of P. brassicae pathotypes 3 and 6 (Pb3 and Pb6) that differ in their host range. Pb3 is highly virulent on B. napus (but also infects other Brassica species) while Pb6 infects only vegetable Brassica crops. Both the Pb3 and Pb6 genomes are highly compact, each with a total size of 24.2 Mb, and contain less than 2 % repetitive DNA. Clustering of genome-wide single nucleotide polymorphisms (SNP) of Pb3, Pb6 and three additional re-sequenced pathotypes (Pb2, Pb5 and Pb8) shows a high degree of correlation of cluster grouping with host range. The Pb3 genome features significant reduction of intergenic space with multiple examples of overlapping untranslated regions (UTRs). Dependency on the host for essential nutrients is evident from the loss of genes for the biosynthesis of thiamine and some amino acids and the presence of a wide range of transport proteins, including some unique to P. brassicae. The annotated genes of Pb3 include those with a potential role in the regulation of the plant growth hormones cytokinin and auxin. The expression profile of Pb3 genes, including putative effectors, during infection and their potential role in manipulation of host defence is discussed.
Conclusion The P. brassicae genome sequence reveals a compact genome, a dependency of the pathogen on its host for some essential nutrients and a potential role in the regulation of host plant cytokinin and auxin. Genome annotation supported by RNA sequencing reveals significant reduction in intergenic space which, in addition to low repeat content, has likely contributed to the P. brassicae compact genome.See it on Scoop.it, via MycorWeb Plant-Microbe Interactions
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

There and Back Again: Parallel Evolution of Cell Coverings in Centrohelid Heliozoans

There and Back Again: Parallel Evolution of Cell Coverings in Centrohelid Heliozoans | Protist evolution and biology | Scoop.it

Publication date: February 2016
Source:Protist, Volume 167, Issue 1
Author(s): Vasily V. Zlatogursky
Centrohelid heliozoans are non-ciliary axopodial protists of uncertain affinities.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa)

Publication date: July 2015 Source:Protist, Volume 166, Issue 3 Author(s): Yasuhide Nakamura, Ichiro Imai, Atsushi Yamaguchi, Akihiro Tuji, Fabrice Not, Noritoshi Suzuki Phaeodarians are a group of widely distributed marine...

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Do All Dinoflagellates have an Extranuclear Spindle?

Do All Dinoflagellates have an Extranuclear Spindle? | Protist evolution and biology | Scoop.it

Publication date: November 2015
Source:Protist, Volume 166, Issue 5
Author(s): Eunyoung Moon, Seung Won Nam, Woongghi Shin, Myung Gil Park, D.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

BIR Pipeline for Preparation of Phylogenomic Data

BIR Pipeline for Preparation of Phylogenomic Data | Protist evolution and biology | Scoop.it

Authors: Surendra Kumar, Anders K. Krabberød, Ralf S. Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang and Kamran Shalchian-Tabrizi


Summary: We present a pipeline named BIR (Blast, Identify and Realign) developed for phylogenomic analyses. BIR is intended for the identification of gene sequences applicable for phylogenomic inference. The pipeline allows users to apply their own manually curated sequence alignments (seed) in search for homologous genes in sequence databases and available genomes. BIR automatically adds the identified sequences from these databases to the seed alignments and reconstruct a phylogenetic tree from each. The BIR pipeline is an efficient tool for the identification of orthologous gene copies because it expands user-defined sequence alignments and conducts massive parallel phylogenetic reconstruction. The application is also particularly useful for large-scale sequencing projects that require management of a large number of single-gene alignments for gene comparison, functional annotation, and evolutionary analyses.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Phylogenomic Analysis of “Red” Genes from Two Divergent Species of the “Green” Secondary Phototrophs, the Chlorarachniophytes, Suggests Multiple Horizontal Gene Transfers from the Red Lineage befor...

Phylogenomic Analysis of “Red” Genes from Two Divergent Species of the “Green” Secondary Phototrophs, the Chlorarachniophytes, Suggests Multiple Horizontal Gene Transfers from the Red Lineage befor... | Protist evolution and biology | Scoop.it
The plastids of chlorarachniophytes were derived from an ancestral green alga via secondary endosymbiosis. Thus, genes from the “green” lineage via secondary endosymbiotic gene transfer (EGT) are expected in the nuclear genomes of the Chlorarachniophyta. However, several recent studies have revealed the presence of “red” genes in their nuclear genomes. To elucidate the origin of such “red” genes in chlorarachniophyte nuclear genomes, we carried out exhaustive single-gene phylogenetic analyses, including two operational taxonomic units (OTUs) that represent two divergent sister lineages of the Chlorarachniophyta, Amorphochlora amoeboformis ( = Lotharella amoeboformis ; based on RNA sequences newly determined here) and Bigelowiella natans (based on the published genome sequence). We identified 10 genes of cyanobacterial origin, phylogenetic analysis of which showed the chlorarachniophytes to branch with the red lineage (red algae and/or red algal secondary or tertiary plastid-containing eukaryotes). Of the 10 genes, 7 demonstrated robust monophyly of the two chlorarachniophyte OTUs. Thus, the common ancestor of the extant chlorarachniophytes likely experienced multiple horizontal gene transfers from the red lineage. Because 4 of the 10 genes are obviously photosynthesis- and/or plastid-related, and almost all of the eukaryotic OTUs in the 10 trees possess plastids, such red genes most likely originated directly from photosynthetic eukaryotes. This situation could be explained by a possible cryptic endosymbiosis of a red algal plastid before the secondary endosymbiosis of the green algal plastid, or a long-term feeding on a single (or multiple closely related) red algal plastid-containing eukaryote(s) after the green secondary endosymbiosis.
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 pyrosequencing - Egge - Journal of Eukaryotic Microbiology - Wiley Online Library

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 pyrosequencing - Egge - Journal of Eukaryotic Microbiology - Wiley Online Library | Protist evolution and biology | Scoop.it

Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for two years, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From c. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity.

  
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

IWOP 2014

IWOP 2014 | Protist evolution and biology | Scoop.it
The 13th International Workshop on Opportunistic Protists is planned for November 13-15, 2014 in Seville, Spain http://t.co/dnHZL3jxz7
more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution

Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution | Protist evolution and biology | Scoop.it

Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.

more...
No comment yet.
Scooped by Anders Kristian Krabberød
Scoop.it!

Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome

Genome sequencing of Symbiodinium minutum revealed that 95 of 109 plastid-associated genes have been transferred to the nuclear genome and subsequently expanded by gene duplication. Only 14 genes remain in plastids and occur as DNA minicircles. Each minicircle (1.8-3.3 kb) contains one gene and a conserved non-coding region containing putative promoters and RNA-binding sites. Nine types of RNA editing, including a novel G/U type, were discovered in minicircle transcripts, but not in genes transferred to the nucleus. In contrast to DNA editing sites in dinoflagellate mitochondria, which tend to be highly conserved across all taxa, editing sites employed in DNA minicircles are highly variable from species to species. Editing is crucial for core photosystem protein function. It restores evolutionarily conserved amino acids and increases peptidyl hydropathy. It also increases protein plasticity necessary to initiate photosystem complex assembly.

more...
No comment yet.