<i>UniEuk</i>: Time to Speak a Common Language in Protistology!

Berney, Cédric; Ciuprina, Andreea; Bender, Sara J.; Brodie, Juliet; Edgcomb, Virginia P.; Kim, Eun-Soo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina M.; Audic, Stéphane; Bass, David; Caron, David A.; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z.; Simpson, Alastair G. B.; Stamatakis, Alexandros; Campo, Javier del; Yilmaz, Pelin; Vargas, Colomban de

doi:10.1111/jeu.12414

Cited by 74 publications

(71 citation statements)

References 12 publications

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“…As environmental conditions selectively favor the growth of specific taxa at smaller scales, it is not surprising to find statistically different fungal communities associated with larger distinct oceanographic regions. Though these phylogenetically classified sequences are informative, more distance-based analysis, such as those being generated through UniEuk (Berney et al 2017) will help to more accurately elucidate biogeography.…”

Section: Marine Fungal Community Analysis Using 18s Rrna Genesmentioning

confidence: 99%

Global diversity and geography of planktonic marine fungi

et al. 2019

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Growing interest in understanding the relevance of marine fungi to food webs, biogeochemical cycling, and biological patterns necessitates establishing a context for interpreting future findings. To help establish this context, we summarize the diversity of cultured and observed marine planktonic fungi from across the world. While exploring this diversity, we discovered that only half of the known marine fungal species have a publicly available DNA locus, which we hypothesize will likely hinder accurate highthroughput sequencing classification in the future, as it does currently. Still, we reprocessed >600 high-throughput datasets and analyzed 4.9 × 10 9 sequences (4.8 × 10 9 shotgun metagenomic reads and 1.0 × 10 8 amplicon sequences) and found that every fungal phylum is represented in the global marine planktonic mycobiome; however, this mycobiome is generally predominated by three phyla: the Ascomycota, Basidiomycota, and Chytridiomycota. We hypothesize that these three clades are the most abundant due to a combination of evolutionary histories, as well as physical processes that aid in their dispersal. We found that environments with atypical salinity regimes (>5 standard deviations from the global mean: Red Sea, Baltic Sea, sea ice) hosted higher proportions of the Chytridiomycota, relative to open oceans that are dominated by Dikarya. The Baltic Sea and Mediterranean Sea had the highest fungal richness of all areas explored. An analysis of similarity identified significant differences between oceanographic regions. There were no latitudinal gradients of marine fungal richness and diversity observed. As more high-throughput sequencing data become available, expanding the collection of reference loci and genomes will be essential to understanding the ecology of marine fungi.

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Section: Marine Fungal Community Analysis Using 18s Rrna Genesmentioning

confidence: 99%

Global diversity and geography of planktonic marine fungi

et al. 2019

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“…In a second set of experiments, we used a large dataset from the UniEuk project (Berney et al, 2017) as a showcase for deploying on a standard parallel compute cluster. For this test, we used a phylogenetic placement of 585, 050 QS on a reference tree comprising 800 taxa, which resulted from an OTU clustering of roughly 300 million sequences (respective article in press).…”

Section: Discussionmentioning

confidence: 99%

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

Barbera

Czech

Lutteropp

et al. 2020

Preprint

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1Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing 2 and the improving accuracy of data analysis methods. One such analysis method is phylogenetic 3 placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a 4 sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample 5 remains challenging, as traditional methods do not scale well with the increasing data volumes and/or 6 do not leverage the phylogenetic placement information. 7Here, we present SCRAPP, a highly parallel and scalable tool that uses a molecular species delimitation 8 algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic 9 placement of the sample. SCRAPP employs a novel approach to cluster phylogenetic placements, called 10 placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data 11 volumes. Furthermore, it utilizes the phylogeny-aware molecular species delimitation method mPTP to 12 quantify diversity. 13 We evaluated SCRAPP using both, simulated and empirical datasets. We use simulated data to verify 14 our approach. Tests on an empirical dataset show that SCRAPP-derived metrics can classify samples 15 by their diversity-correlated features equally well or better than existing, commonly used approaches. 16SCRAPP is available at https: / / github .com/ pbdas/ scrapp 17

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“…The enormous diversity of unicellular organisms, the augmented knowledge we have about their morphology, ecology and life cycles together with the “revolution” of molecular approaches call for establishing a common taxonomic framework (e.g., Berney et al., ). Phylogenetic studies and metabarcoding approaches will provide important information in this direction in the coming years.…”

Section: Discussionmentioning

confidence: 99%

dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

Mordret

Piredda

Vaulot

et al. 2018

Molecular Ecology Resources

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Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity.

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UniEuk: Time to Speak a Common Language in Protistology!

Cited by 74 publications

References 12 publications

Global diversity and geography of planktonic marine fungi

Global diversity and geography of planktonic marine fungi

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene

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