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The anti-neural role of BMP signaling is a consequence of its ancestral function in dorsoventral patterning.

Code ↔ Paper

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  1. [1] § Materials and methods › Inhibitor treatments, bulk RNA-seq, de novo transcriptome assembly and differential gene expression analysis in Stomolophus ↔ deseq.R, the whole file · a weak match · score 0.60 · DESeq2, Kallisto, importing, tximport, Trinity, transcriptomes · Report a mismatch
  2. [2] § Materials and methods › Single-cell RNA-seq analysis ↔ scRNA-seqDotplots_Fig2_FigS4.R, lines 100 to 175 · score 0.57 · DotPlot, ID.separate, SEM, SD, subset, raw · Report a mismatch

Paper

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The authors' code

R · 45 lines · 1.9 KB · no license · 1 match

  1. library(tidyverse)
  2. library(tximport)
  3. library(DESeq2)
  4. library(readr)
  5. # Prepare your data
  6. annot <- read_tsv("nv2.func-04.04.23.tsv")
  7. tx2geneFile <- "Trinity.fasta.gene_trans_map"
  8. tx2gene <- read.table(tx2geneFile, header = FALSE, col.names = c("gene_id", "transcript_id"))
  9. tx2gene <- select(tx2gene, c(2,1))
  10. samples <- list.dirs("kallisto", full.names = FALSE, recursive = FALSE)
  11. files <- file.path("kallisto", samples, "abundance.tsv")
  12. names(files) <- samples
  13. sample_metadata <- data.frame(row.names = samples, condition = gsub("[0-9]+$", "", samples))
  14. # import best blast hits and filter
  15. bbh <- read_tsv("stomolophus_nv2.map.renamed.m8", col_names=FALSE)
  16. names(bbh)<- c("query", "target", "pident", "alnlen", "mismatch", "gapopen", "qstart", "qend", "tstart", "tend", "evalue", "bits", "qlen", "tlen")
  17. bbh <- bbh %>% filter(evalue <= 1e-2) %>% group_by(query) %>% arrange(desc(bits)) %>%
  18. filter(row_number()==1) %>% ungroup()
  19. # Import transcript-level estimates and summarize to gene-level
  20. # This preserves the fractional nature of the counts
  21. txi <- tximport(files,
  22. type = "kallisto",
  23. tx2gene = tx2gene, # transcript-to-gene mapping file
  24. countsFromAbundance = "no") # Keeps original estimated counts
  25. # Create DESeq2 dataset directly from tximport object
  26. # DESeq2 internally handles these fractional counts appropriately
  27. dds <- DESeqDataSetFromTximport(txi,
  28. colData = sample_metadata,
  29. design = ~ condition)
  30. # Run DESeq2 - it knows how to work with these counts
  31. dds <- DESeq(dds)
  32. res <- results(dds, contrast = c("condition", "SD", "SK"))
  33. res <- as_tibble(res, rownames="gene")
  34. # join with best blast hits
  35. res <- left_join(res, bbh, by=c("gene"="query"))
  36. res <- res %>% filter(padj<=0.05) %>% left_join(annot %>%
  37. select(geneID,gene_short_name,cdsName), by=c("target"="geneID"))
  38. write_tsv(res, "DEG_results_all.csv")

deseq.R at commit 1b6c738, no license · at the source

Overview

Authors: Paul Knabl1,2,3, June F Ordoñez2,4, Juan Daniel Montenegro Cabrera1, Daniel Abed-Navandi5, Roland Halbauer6, Oliver Link1,2, Tim Wollesen4, Grigory Genikhovich1
  1. Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
  2. Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
  3. Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
  4. Department of Evolutionary Biology, University of Vienna, Vienna, Austria
  5. Haus des Meeres, Vienna, Austria
  6. Tiergarten Schönbrunn, Vienna, Austria
Journal: PLoS biology, volume 24, issue 5, article e3003803
Dates: received 9 June 2025; accepted 4 May 2026; published online 21 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003803 · PMID 42166538 · PMCID PMC13193452 · OpenAlex W7162018997
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: other (organism)
Methods: Connectivity
MeSH: Body Patterning*, Bone Morphogenetic Proteins*, Signal Transduction*, Animals, Animals, Genetically Modified, Central Nervous System, Cnidaria, Gene Expression Regulation, Developmental, Neurogenesis, Neurons (* major topic)
Topic: Marine Invertebrate Physiology and Ecology (Animal Science and Zoology, Agricultural and Biological Sciences), according to OpenAlex
Citations: cited by 2 papers (Europe PMC); 105 references in the paper

Abstract

In Bilateria with centralized nervous systems (e.g., in vertebrates or arthropods), the minimum of the BMP signaling activity gradient defines the position of the central nervous system. BMP-dependent patterning of the secondary body axis is ancestral for Bilateria and possibly also for the bilaterian sister clade Cnidaria. However, the variety of levels of centralization of the nervous systems in Bilateria—from diffuse to fully centralized—as well as the lack of centralization of the nervous system in Cnidaria, suggest that BMP signaling cannot be perceived as a universally “anti-neural” signal. Here we use transgenic reporter lines in the anthozoan cnidarian Nematostella to show that BMP signaling is active in distinct neuronal populations. Moreover, attenuation of BMP signaling followed by RNA-Seq shows that BMP signaling is a positive regulator of many neuronal genes, including the top-tier neural progenitor marker soxB(2). Furthermore, we analyze BMP signaling activity in the cubozoan jellyfish Tripedalia and the scyphozoan jellyfish Stomolophus and prove that BMP signaling in parts of the diffuse nervous system is not an anthozoan but an ancestral cnidarian feature, shared by anthozoans and medusozoans. Finally, we show that the highly centralized ventral nervous system of the nonmodel spiralian, the chaetognath Spadella, forms out of paired BMP signaling-positive domains on the lateral sides of the embryo. Together, our data suggest that one of the ancestral roles of BMP signaling may have been in promoting neurogenesis. We propose that the “anti-neural” function of BMP signaling in vertebrates and arthropods is a consequence of its global role in the dorsoventral patterning of the ectoderm.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

Zenodo 19686897

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the supplementary material
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), Seurat (2 files), tidyverse (2 files)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
3 files

genikhovich-lab/data-for-plots

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 1a38a5fdedd679c10bafb980d6b3cbb9f2869617, 21 April 2026
Languages: R (2)
Size: 8 files, 2 scripts
Software Heritage: not archived
Found in: the text, “Single-cell RNA-seq analysis”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), Seurat (2 files), tidyverse (2 files)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
3 files

Genikhovich-Lab/Stomolophus

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 1b6c738bb0cc0d94f066edaa41c09a8003f94dfb, 25 March 2026
Languages: R (1)
Size: 32 files, 1 script
Software Heritage: not archived
Found in: the text, “Inhibitor treatments, bulk RNA-seq, de novo tran”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: DESeq2 (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
2 files

Zenodo 19686882

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data Availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: DESeq2 (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
2 files

Genikhovich-Lab

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Data Availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)

The paper's code and data availability statement is in the Data section.

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Data

Datasets cited

Other data links

Data Availability

Newly generated sequencing data is deposited as bioprojects at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1269470 and http://www.ncbi.nlm.nih.gov/bioproject/1441074. All code required to reproduce the computational analyses of this study can be found on https://github.com/Genikhovich-Lab/ and, additionally, at 10.5281/zenodo.19686897 (https://doi.org/10.5281/zenodo.19686897) and 10.5281/zenodo.19686882 (https://doi.org/10.5281/zenodo.19686882). All other relevant data are within the paper and its Supporting information files.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 2, 28 September 2026

  • Funding: added Österreichischen Akademie der Wissenschaften; Austrian Science Fund: P 34665, P32705, PAT2395824; Universität Wien; Universitetet i Bergen; Lomonosov Moscow State University

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 10 MeSH terms, 105 references.

Cite

This paper

Knabl, P., Ordoñez, J. F., Montenegro Cabrera, J. D., Abed-Navandi, D., Halbauer, R., Link, O., Wollesen, T., & Genikhovich, G. (2026). The anti-neural role of BMP signaling is a consequence of its ancestral function in dorsoventral patterning. PLoS biology, 24(5), e3003803. https://doi.org/10.1371/journal.pbio.3003803

BibTeX

@article{knabl2026anti,
author = {Knabl, Paul and Ordoñez, June F and Montenegro Cabrera, Juan Daniel and Abed-Navandi, Daniel and Halbauer, Roland and Link, Oliver and Wollesen, Tim and Genikhovich, Grigory},
title = {{The anti-neural role of BMP signaling is a consequence of its ancestral function in dorsoventral patterning}},
journal = {PLoS biology},
year = {2026},
month = may,
volume = {24},
number = {5},
pages = {e3003803},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003803},
url = {https://doi.org/10.1371/journal.pbio.3003803},
pmid = {42166538},
pmcid = {PMC13193452}
}

RIS

TY - JOUR
AU - Knabl, Paul
AU - Ordoñez, June F
AU - Montenegro Cabrera, Juan Daniel
AU - Abed-Navandi, Daniel
AU - Halbauer, Roland
AU - Link, Oliver
AU - Wollesen, Tim
AU - Genikhovich, Grigory
TI - The anti-neural role of BMP signaling is a consequence of its ancestral function in dorsoventral patterning
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/05/21
VL - 24
IS - 5
SP - e3003803
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003803
UR - https://doi.org/10.1371/journal.pbio.3003803
LA - en
ER -

CSL-JSON

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