Evidence map›Paper›PMID 41211940›Full record

ArticleJournal of phycology2025

Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.

Wade R Roberts, Matthew Parks, Marissa Ashner, Matthew P Ashworth, Nina Denne, Elizabeth C Ruck, Elias Spiliotopoulos, Anni Wang, Shady A Amin, Sarah Schaack and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of phycology, 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

12 authors.

Wade R RobertsDepartment of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA.ORCID https://orcid.org/0000-0002-5100-7558
Matthew ParksDepartment of Biology, University of Central Oklahoma, Edmond, Oklahoma, USA.ORCID https://orcid.org/0000-0002-9366-7001
Marissa AshnerDepartment of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois, USA.
Matthew P AshworthDepartment of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.ORCID https://orcid.org/0000-0002-4162-2004
Nina DenneBiology Department, Carleton College, Northfield, Minnesota, USA.
Elizabeth C RuckDepartment of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA.ORCID https://orcid.org/0000-0002-9288-1989
Elias SpiliotopoulosBiology Department, Reed College, Portland, Oregon, USA.ORCID https://orcid.org/0000-0002-8522-2459
Anni WangDepartment of Biological Science, Florida State University, Tallahassee, Florida, USA.
Shady A AminBiology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.ORCID https://orcid.org/0000-0003-3780-8102
Sarah SchaackBiology Department, Reed College, Portland, Oregon, USA.ORCID https://orcid.org/0000-0002-7297-1565
Norman J WickettDepartment of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.ORCID https://orcid.org/0000-0003-0944-1956
Andrew J AlversonDepartment of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA.ORCID https://orcid.org/0000-0003-1241-2654

Funding

Division of Environmental Biology 1353131Division of Environmental Biology 1353152Division of Environmental Biology 2331644Division of Environmental Biology 2336342Division of Molecular and Cellular Biosciences 1150213
6 · The paper itself

Abstract

We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.

Indexed as

DiatomsEvolution, MolecularGenome, BacterialGenome SizeMetagenomeBacteriaGenomearaphiddiatomsmetagenomephycospherePsammoneis

Identifiers

PMID41211940
PMCPMC12718438

What OpenQuestion holds

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Registered trials

None linked

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.