EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Campo, Javier del; Kolísko, Martin; Boscaro, Vittorio; Santoferrara, Luciana F.; Massana, Ramón; Guillou, Laure; Simpson, Alastair G. B.; Berney, Cédric; Vargas, Colomban de; Brown, Matthew W.; Keeling, Patrick J.; Parfrey, Laura Wegener

doi:10.1101/278085

Cited by 37 publications

(40 citation statements)

References 33 publications

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“…C). If necessary, the names of hierarchically higher (broader) taxa were propagated so that each taxonomic string had the same number of elements (for practical reasons, traditional taxonomic ranks were not used in building the database; del Campo et al ., ).…”

Section: Methodsmentioning

confidence: 97%

“…Following EukRef guidelines (eukref.org;del Campo et al, 2018; Fig. 1A), a raw SSU rRNA gene sequence dataset for each group was obtained using the eukref_gbretrieve.py script.…”

Section: Sequence Retrieval and Curationmentioning

confidence: 99%

“…The EukRef Initiative (eukref.org;del Campo et al, 2018) is a community effort to provide a publicly available reference dataset of eukaryotic SSU rRNA gene sequences. Phylogenetic trees and taxonomic annotations, curated by experts of each taxonomic group, will be freely shared online and integrated with other commonly used databases, such as SILVA (Quast et al, 2013) and PR 2 (Guillou et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

Boscaro

Santoferrara

Zhang

et al. 2018

Environmental Microbiology

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High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.

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Section: Methodsmentioning

confidence: 97%

“…Following EukRef guidelines (eukref.org;del Campo et al, 2018; Fig. 1A), a raw SSU rRNA gene sequence dataset for each group was obtained using the eukref_gbretrieve.py script.…”

Section: Sequence Retrieval and Curationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

Boscaro

Santoferrara

Zhang

et al. 2018

Environmental Microbiology

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“…arguably at the genus level or above). Our reference phylogenetic tree can be therefore considered as a useful tool to approach new ecological and evolutionary questions (Pan et al, 2017) and classify the unknown sequences (Mahé et al, 2017) like it has already been done for other groups of eukaryotic microorganisms (del Campo et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…The reference phylogenetic tree was built with a similar pipeline as proposed by del Campo et al (2018). Briefly, sequences related to Trebouxiophyceae were extracted from SILVA v132 database (Quast et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches

Metz

Domaizon

Unrein

et al. 2019

Environmental Microbiology

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Summary Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free‐living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free‐living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.

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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

Sahraei

Furneaux

Kluting

et al. 2022

Ecology and Evolution

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Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large‐scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic‐dry part that has a species rich grass‐dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%–40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.

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EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Cited by 37 publications

References 33 publications

EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

EukRef‐Ciliophora: a manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates

Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

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