Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38649807", "kind": "science-record", "revision": 5, "content_hash": "sha256:ae6f097a368890435ea32b878374140809210d914da6bf33fc34710cb4b0aa16", "created_at": "2026-11-01T19:20:37Z", "updated_at": "2026-11-01T22:54:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek.", "doi": "10.1186/s12864-024-10253-x", "pmid": "38649807", "authors": ["Sara Lamei Javan", "Arman Beyraghdar Kashkooli", "AbdolAli Shojaeiyan", "Sina Majidian"], "journal": "BMC genomics", "year": 2024, "abstract": "Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting agents which involves in manipulation of metabolite and biochemical pathways stimulating defense responses. Methyl jasmonate elicitor was used to increase diosgenin biosynthesis in fenugreek plants. However, the molecular mechanism and gene expression profiles underlying diosgening accumulation remain unexplored. In the current study we performed an extensive analysis of publicly available RNA-sequencing datasets to elucidate the biosynthesis and expression profile of fenugreek plants treated with methyl jasmonate. For this purpose, seven read datasets of methyl jasmonate treated plants were obtained that were covering several post-treatment time points (6-120 h). Transcriptomics analysis revealed upregulation of several key genes involved in diosgenein biosynthetic pathway including Squalene synthase (SQS) as the first committed step in diosgenin biosynthesis as well as Squalene Epoxidase (SEP) and Cycloartenol Synthase (CAS) upon methyl jasmonate application. Bioinformatics analysis, including gene ontology enrichment and pathway analysis, further supported the involvement of these genes in diosgenin biosynthesis. The bioinformatics analysis led to a comprehensive validation, with expression profiling across three different fenugreek populations treated with the same methyl jasmonate application. Initially, key genes like SQS, SEP, and CAS showed upregulation, followed by later upregulation of Δ24, suggesting dynamic pathway regulation. Real-time PCR confirmed consistent upregulation of SQS and SEP, peaking at 72 h. Additionally, candidate genes Δ24 and SMT1 highlighted roles in directing metabolic flux towards diosgenin biosynthesis. This integrated approach validates the bioinformatics findings and elucidates fenugreek's molecular response to methyl jasmonate elicitation, offering insights for enhancing diosgenin yield. The assembled transcripts and gene expression profiles are deposited in the Zenodo open repository at https://doi.org/10.5281/zenodo.8155183 .", "claims": [{"id": "claim-method", "statement": "To estimate DEGs, the deseq2 package v1.38 in R was used, resulting in the fold changes and p-values [24].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38649807", "locator": "sections[15] \"Differential expression gene analysis\" paragraph 2", "quote": "To estimate DEGs, the deseq2 package v1.38 in R was used, resulting in the fold changes and p-values [24]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the Zenodo open repository at 10.5281/zenodo.8155183 and the NCBI database at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA508420.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38649807", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The datasets analyzed during the current study are available in the Zenodo open repository at 10.5281/zenodo.8155183 and the NCBI database at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA508420."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Real-time PCR validated the consistent upregulation of SQS and SEP, with expression peaking at 72 hours after methyl jasmonate treatment.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38649807", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Real-time PCR confirmed consistent upregulation of SQS and SEP, peaking at 72 h."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Real-time PCR validated the consistent upregulation of SQS and SEP, with expression peaking at 72 hours after methyl jasmonate treatment.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38649807"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA508420"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA508420"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38649807", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-024-10253-x", "sha256": "sha256:e766aeb00c9e766b53e6101107c01cedc1f549e1ac6e356404b0e3c521ac3ffe", "bytes": 40011, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-024-10253-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11034138", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA508420", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA508420", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA508420", "version": null, "note": "The datasets analyzed during the current study are available in the Zenodo open repository at 10.5281/zenodo.8155183 and the NCBI database at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA508420.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Zenodo open repository at 10.5281/zenodo.8155183 and the NCBI database at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA508420.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PRJNA508420 not downloaded", "asset:data:geo:PRJNA508420 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To estimate DEGs, the deseq2 package v1.38 in R was used, resulting in the fold changes and p-values [24]."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PRJNA508420"], "resolved_accessions": [], "statements": ["The datasets analyzed during the current study are available in the Zenodo open repository at 10.5281/zenodo.8155183 and the NCBI database at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA508420."], "basis": "The paper names PRJNA508420, but the accession does not resolve in the repository (not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:38649807", "data:geo:PRJNA508420"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJNA508420"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:16:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11374, "completion_tokens": 1248, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38649807", "type": "paper", "label": "pmid:38649807"}, {"id": "source:pmid:38649807", "type": "manuscript", "label": "PMID 38649807 full text"}, {"id": "data:geo:PRJNA508420", "type": "dataset", "label": "GEO PRJNA508420"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38649807", "type": "paper", "label": "pmid:38649807"}, {"id": "source:pmid:38649807", "type": "manuscript", "label": "PMID 38649807 full text"}, {"id": "data:geo:PRJNA508420", "type": "dataset", "label": "GEO PRJNA508420"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38649807", "type": "extraction", "used": ["source:pmid:38649807"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJNA508420", "type": "accession_resolution", "used": ["data:geo:PRJNA508420"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38649807", "parent_hash": "sha256:7ff476f51d0a1c4fe5d20f4372ebc5f6e01315701d47d5c539124415504e3e20", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PRJNA508420 licence not read", "asset:data:geo:PRJNA508420 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["Δ24, suggesting dynamic pathway regulation. Real-time PCR confirmed consistent upregulation of SQS and"], "order_basis": "paper_text_order:1914", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To estimate DEGs, the deseq2 package v1.38 in R was used, resulting in the fold changes and p-values [24]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}