Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data

Grattepanche, Jean‐David; Walker, Laura M.; Ott, Brittany M.; Pinto, Daniela Lopes Paim; Delwiche, Charles F.; Lane, Christopher E.; Katz, Laura A.

doi:10.1002/bies.201700198

Cited by 52 publications

(50 citation statements)

References 136 publications

(187 reference statements)

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“…Key characteristics of Opisthokonta include synthesis of extracellular chitin, cyst/spore/cell walls of filamentous growth, hyphae, and the extracellular digestion of substrates (Adl et al, 2018). Only 5% of SAR are from well sampled families making them a poorly understood phyla (Grattepanche et al, 2018). SAR is made up of Stramenopila, Alveolate, and Rhizaria.…”

Section: Discussionmentioning

confidence: 99%

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

Tobias-Hünefeldt

Wing

Espinel-Velasco

et al. 2019

Preprint

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SummarySystems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

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Section: Discussionmentioning

confidence: 99%

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

Tobias-Hünefeldt

Wing

Espinel-Velasco

et al. 2019

Preprint

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“…Most importantly, it confirms that Telonemia is a bona fide eukaryotic phylum, at the same phylogenetic level as other major phyla such as the Sar members (Stramenopila, Alveolata, and Rhizaria) (Burki et al 2007;Hackett et al 2007;Rodriguez-Ezpeleta, Brinkmann, Burger, et al 2007 . Telonemia thus appears crucial for understanding the early evolution of the Sar group, a globally distributed and highly diverse assemblage of eukaryotes likely containing the majority of protist lineages (del Campo et al 2014;de Vargas et al 2015;Grattepanche et al 2018).…”

Section: Discussionmentioning

confidence: 99%

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

Strassert

Jamy

Mylnikov

et al. 2018

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The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these 'orphan' groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments.Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using siteheterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker 'TSAR' to accommodate this new megaassemblage in the phylogeny of eukaryotes. supporting a sister relationship to Telonemia + Sar; for details, see fig. S1 and fig. S2).

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“…The SAR supergroup contains a high diversity of lineages that include many important photosynthetic lineages (e.g. diatoms and kelp), and important parasites of animals (e.g., Plasmodium , the causative agent of malaria) and plants (e.g., oomycetes, or water molds) (26). Phytophthora is a large oomycete genus (>160 species found to date) and contains some of the most devastating plant pathogens that destroy a wide range of plants important in agriculture, forestry, ornamental and recreational plantings, and natural ecosystems (27).…”

Section: Introductionmentioning

confidence: 99%

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

Fang

Coelho

Shu

et al. 2019

Preprint

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26Centromeres are chromosomal regions that serve as platforms for kinetochore assembly 27 and spindle attachments, ensuring accurate chromosome segregation during cell division. 28Despite functional conservation, centromere DNA sequences are diverse and often repetitive, 29 making them challenging to assemble and identify. Here, we describe centromeres in an 30 oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and 31 chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput 32 sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and 33 during nuclear division. We report an improved genome assembly of the P. sojae reference strain, 34 which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. 35By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are 36 regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, 37 and lack the histone modification H3K4me2 but are embedded within regions with the 38 heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia-like 39 transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements 40 are also found in oomycete relatives of P. sojae, and may be applied as a criterion for prediction 41 of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes 42 as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup 43 including diatoms and Plasmodium falciparum that have relatively short and simple regional 44 centromeres. Identification of P. sojae centromeres in turn also augments the genome assembly. 45 46 Significance Statement 49Oomycetes are fungal-like microorganisms that belong to the stramenopiles within the 50 Stramenopila-Alveolata-Rhizaria (SAR) supergroup. The Phytophthora oomycetes are infamous 51 as plant killers, threatening crop production worldwide. Because of the highly repetitive nature of 52 their genomes, assembly of oomycete genomes presents challenges that impede identification of 53 centromeres, which are chromosomal sites mediating faithful chromosome segregation. We 54 report long-read sequencing-based genome assembly of the Phytophthora sojae reference strain, 55 which facilitated the discovery of centromeres. P. sojae harbors large regional centromeres 56 enriched for a Copia-like transposon that is also found in discrete clusters in other oomycetes. 57This study provides insight into the oomycete genome organization, and broadens our knowledge 58 of the centromere structure, function and evolution in eukaryotes. 59 60 Accurate segregation of chromosomes during mitosis and meiosis is critical for the 61 development and reproduction of all eukaryotic organisms. Centromeres are specialized regions 62 of chromosomes that mediate kinetochore formation, spindle attachment, and sister chromatid 63 segregation during cell division (1, 2). T...

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Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data

Cited by 52 publications

References 136 publications

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

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