Evidence map›Paper›PMID 41339349›Full record

ArticleScientific data2025

A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes.

Allison Coe, James I Mullet, Nhi N Vo, Paul M Berube, Maya I Anjur-Dietrich, Eli Salcedo, Sierra M Parker, Konnor VonEmster, Christina Bliem, Aldo A Arellano and 3 more

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Allison Coe *Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. a_coe@mit.edu.ORCID 0000-0003-0561-4573
James I Mullet *Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Nhi N Vo *Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Paul M BerubeDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0001-5598-6602
Maya I Anjur-DietrichDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Eli SalcedoDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Sierra M ParkerDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Konnor VonEmsterDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Christina BliemDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Aldo A ArellanoDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Kurt G CastroDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0009-0007-8608-1903
Jamie W BeckerDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0001-5308-1818
Sallie W ChisholmDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0003-1480-2445

Funding

Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation) GBMF495National Science Foundation (NSF) DBI-0424599National Science Foundation (NSF) OCE-1153588National Science Foundation (NSF) OCE-2048470Simons Foundation 329108Simons Foundation 337262Simons Foundation 984601
6 · The paper itself

Abstract

Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.

Indexed as

Bacterial ProteinsMetagenomeProchlorococcusSynechococcusGenome, BacterialMetagenomicsPhylogenyBacterial Proteins

Identifiers

PMID41339349
PMCPMC12675747

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.