Rubber Biosynthesis Focus

A pathway-centered entry for MVA/MEP, IPP/DMAPP, prenyl donors, CPT/CPTL, REF/SRPP, latex/root-associated and terpenoid candidate genes.

This topic is built from precomputed GFF/GO/KEGG/homology candidate sets and linked evidence from expression, proteome, localization, Pfam, Swiss-Prot, PPI, coexpression and TFBS modules. Results are candidate evidence, not experimental validation.

The current database contains 5523 candidate records, 4979 candidate genes, and 8 pathway steps; the main display is centered on the TK1151 reference while OH-1004/LXL04 remains queryable and linked.

Examples TkA01G624900 LXL04_000258

Download current filtered candidate TSV

Cross-species Research Reference

9 reference genes are counted separately from rubber-dandelion candidates. They are literature, omics, or sequence resources from Para rubber tree, guayule, a related dandelion, and Eucommia; external function or homology is not direct validation in rubber dandelion.

1. Choose a speciesClick a species card or use the filter to focus on one reference species and material context.

2. Read the evidence typeRead the evidence and boundary column: direct experiments, omics associations, and sequence resources have different interpretation ranges.

3. Verify the sourceEach DOI, article, or public database entry is clickable; download the current filter for further comparison.

Eucommia records are a trans-polyisoprene comparator only and are excluded from natural cis-rubber candidate and pathway-card counts.

9GuayuleClick to view · 4 sources · cis-1,4-polyisoprene

Download current cross-species reference TSV

Species and material	Reference gene / sequence ID	Pathway step	Evidence and boundary	Source
GuayuleParthenium argentatumcis-1,4-polyisoprenePI478663 and heterologous systems	`PaCBP`MF688938;ATD87120CPTL	CPT/CPTL branchGuayule CPT-complex helper subunit	A_direct_experiment PaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary. Helper-subunit evidence must retain the assay context.	10.3389/fpls.2019.00165Characterization of cis-prenyltransferases and cis-prenyltransferase-like protein from guayule
GuayuleParthenium argentatumcis-1,4-polyisoprenePI478663 and heterologous systems	`PaCPT1`MF688933;ATD87115CPT	CPT/CPTL branchForms a cis-prenyltransferase complex with PaCBP	A_direct_experiment PaCPT1 and PaCBP formed an active cis-prenyltransferase complex in heterologous and in-vitro systems. Assay-dependent external evidence; not in-plant rubber-yield proof.	10.3389/fpls.2019.00165Characterization of cis-prenyltransferases and cis-prenyltransferase-like protein from guayule
GuayuleParthenium argentatumcis-1,4-polyisoprenePI478663 and heterologous systems	`PaCPT2`MF688936;ATD87118CPT	CPT/CPTL branchForms a cis-prenyltransferase complex with PaCBP	A_direct_experiment PaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary. Do not equate short-chain in-vitro activity with in-plant rubber yield.	10.3389/fpls.2019.00165Characterization of cis-prenyltransferases and cis-prenyltransferase-like protein from guayule
GuayuleParthenium argentatumcis-1,4-polyisoprenePI478663 and heterologous systems	`PaCPT3`MF688934;ATD87116CPT	CPT/CPTL branchForms a cis-prenyltransferase complex with PaCBP	A_direct_experiment PaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary. Do not equate short-chain in-vitro activity with in-plant rubber yield.	10.3389/fpls.2019.00165Characterization of cis-prenyltransferases and cis-prenyltransferase-like protein from guayule
GuayuleParthenium argentatumcis-1,4-polyisopreneAOS RNAi and overexpression plants	`AOS1`X78166.2CYP74	Latex/root associatedRegulatory candidate associated with rubber content and transferase activity	A_direct_genetic_experiment AOS down-regulation was associated with higher rubber content and rubber-transferase activity. RNAi specificity limitation remains; do not infer a single-gene universal mechanism.	10.3389/fpls.2019.00760Silencing of allene oxide synthase in guayule increases rubber content and rubber transferase activity
GuayuleParthenium argentatumcis-1,4-polyisopreneAZ-3 field bark under well-watered and drought conditions	`PaCBP`PaTc_149493CPTL	CPT/CPTL branchCBP transcript reference in drought transcriptomics	B_omics_association PaCBP was reported in field bark transcriptomics under contrasting irrigation. Association only; transcript abundance is not direct proof of rubber yield.	10.1038/s41598-021-01026-7Transcriptomic analysis of guayule bark under contrasting irrigation conditions
GuayuleParthenium argentatumcis-1,4-polyisopreneAZ-3 field bark under well-watered and drought conditions	`PaCPT1`PaTc_044561CPT	CPT/CPTL branchCPT1 transcript reference in drought transcriptomics	B_omics_association PaCPT1 was reported in field bark transcriptomics under contrasting irrigation. Association only; transcript abundance is not direct proof of rubber yield.	10.1038/s41598-021-01026-7Transcriptomic analysis of guayule bark under contrasting irrigation conditions
GuayuleParthenium argentatumcis-1,4-polyisopreneAZ-3 field bark under well-watered and drought conditions	`PaSRPP1`PaTc_109994SRPP	REF/SRPP rubber-particle proteinsSRPP1 transcript reference in drought transcriptomics	B_omics_association Expression association is not converted into causal rubber-yield evidence. Transcript abundance is not direct proof of rubber yield.	10.1038/s41598-021-01026-7Transcriptomic analysis of guayule bark under contrasting irrigation conditions
GuayuleParthenium argentatumcis-1,4-polyisopreneSRPP1 promoter reporter assay	`PaSRPP1 promoter`PV754023.1SRPP	REF/SRPP rubber-particle proteinsSRPP1 promoter regulatory reference	A_promoter_experiment Promoter sequence is regulatory reference evidence, not a complete gene-model crosswalk. Promoter record is not a complete SRPP1 gene model.	10.1186/s13104-025-07448-0Functional characterization of the guayule SRPP1 promoter

Guayule · PaCBP

Sequence IDMF688938;ATD87120

StepCPT/CPTL branch · CPTL

EvidencePaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary.

BoundaryHelper-subunit evidence must retain the assay context.

Source10.3389/fpls.2019.00165

Guayule · PaCPT1

Sequence IDMF688933;ATD87115

StepCPT/CPTL branch · CPT

EvidencePaCPT1 and PaCBP formed an active cis-prenyltransferase complex in heterologous and in-vitro systems.

BoundaryAssay-dependent external evidence; not in-plant rubber-yield proof.

Source10.3389/fpls.2019.00165

Guayule · PaCPT2

Sequence IDMF688936;ATD87118

StepCPT/CPTL branch · CPT

EvidencePaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary.

BoundaryDo not equate short-chain in-vitro activity with in-plant rubber yield.

Source10.3389/fpls.2019.00165

Guayule · PaCPT3

Sequence IDMF688934;ATD87116

StepCPT/CPTL branch · CPT

EvidencePaCPT/PaCBP complex evidence is displayed with its in-vitro and heterologous-system boundary.

BoundaryDo not equate short-chain in-vitro activity with in-plant rubber yield.

Source10.3389/fpls.2019.00165

Guayule · AOS1

Sequence IDX78166.2

StepLatex/root associated · CYP74

EvidenceAOS down-regulation was associated with higher rubber content and rubber-transferase activity.

BoundaryRNAi specificity limitation remains; do not infer a single-gene universal mechanism.

Source10.3389/fpls.2019.00760

Guayule · PaCBP

Sequence IDPaTc_149493

StepCPT/CPTL branch · CPTL

EvidencePaCBP was reported in field bark transcriptomics under contrasting irrigation.

BoundaryAssociation only; transcript abundance is not direct proof of rubber yield.

Source10.1038/s41598-021-01026-7

Guayule · PaCPT1

Sequence IDPaTc_044561

StepCPT/CPTL branch · CPT

EvidencePaCPT1 was reported in field bark transcriptomics under contrasting irrigation.

BoundaryAssociation only; transcript abundance is not direct proof of rubber yield.

Source10.1038/s41598-021-01026-7

Guayule · PaSRPP1

Sequence IDPaTc_109994

StepREF/SRPP rubber-particle proteins · SRPP

EvidenceExpression association is not converted into causal rubber-yield evidence.

BoundaryTranscript abundance is not direct proof of rubber yield.

Source10.1038/s41598-021-01026-7

Guayule · PaSRPP1 promoter

Sequence IDPV754023.1

StepREF/SRPP rubber-particle proteins · SRPP

EvidencePromoter sequence is regulatory reference evidence, not a complete gene-model crosswalk.

BoundaryPromoter record is not a complete SRPP1 gene model.

Source10.1186/s13104-025-07448-0

Pathway Navigation And Candidate Distribution

MVA · Mevalonate pathway

High 40 · Medium 3 · Low 4 MEP · MEP pathway

High 23 · Medium 0 · Low 36 IPP/DMAPP/FPP · Prenyl-donor metabolism

271

High 141 · Medium 83 · Low 47 CPT/CPTL · Cis-prenyltransferase branch

High 0 · Medium 0 · Low 5 REF/SRPP · Rubber-particle proteins

High 0 · Medium 0 · Low 7 Rubber · Rubber biosynthesis candidates

288

High 1 · Medium 287 · Low 0 Terpenoid · Terpenoid metabolism

380

High 72 · Medium 107 · Low 201 Latex/root · Latex/root associated candidates

4466

High 231 · Medium 1284 · Low 2951

377 MVA/MEP and isoprenoid

Click to filter · High 204 · Medium 86 · Low 87 4466 Latex/root related candidates

Click to filter · High 231 · Medium 1284 · Low 2951 300 Rubber biosynthesis

Click to filter · High 1 · Medium 287 · Low 12 380 Terpenoid metabolism

Click to filter · High 72 · Medium 107 · Low 201

Candidate Genes

2000 candidates match the current filter; 10 are shown per page (page 18 of 200). TSV exports up to 2000 rows under the current filters. Use pathway nodes or summary cards to filter, then inspect Gene Card and linked modules for evidence details.

Gene ID	Pathway/step	Confidence	Evidence layers	Location	Key evidence	Actions
`TkA06G097970` TK1151: TkA06G097970 OH-1004: LXL04_024888	Terpenoid metabolism Terpenoid metabolism	High score 10	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104803.1:101545925-101547031 +	GO:0006720	Gene Card Expression Proteome JBrowse
`TkA06G091990` TK1151: TkA06G091990 OH-1004: LXL04_024977	MVA/MEP and isoprenoid Prenyl-donor metabolism	High score 10	FunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104803.1:103227375-103228292 -	go:0009824 amp dimethylallyltransferase activity molecular_function	Gene Card Expression Proteome JBrowse
`TkA06G086050` TK1151: TkA06G086050 OH-1004: LXL04_025037	MVA/MEP and isoprenoid Mevalonate pathway	High score 10	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104803.1:104470277-104471758 +	GO:0008299	Gene Card Expression Proteome JBrowse
`TkA06G047290` TK1151: TkA06G047290 OH-1004: LXL04_025655	Latex/root related candidates Latex/root associated candidates	High score 10	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104803.1:114805690-114807057 +	go:0006950 response to stress biological_process	Gene Card Expression Proteome JBrowse
`TkA06G029790` TK1151: TkA06G029790 OH-1004: LXL04_026050	MVA/MEP and isoprenoid Mevalonate pathway	High score 10	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104803.1:120151407-120153739 +	GO:0008299	Gene Card Expression Proteome JBrowse
`TkA06G008820` TK1151: TkA06G008820 OH-1004: LXL04_026494	MVA/MEP and isoprenoid Mevalonate pathway	High score 10	FunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104803.1:127347496-127350406 +	go:0004421 hydroxymethylglutaryl-coa synthase activity molecular_function	Gene Card Expression Proteome JBrowse
`TkA04G085780` TK1151: TkA04G085780;TkA06G005680 OH-1004: LXL04_026548	Terpenoid metabolism Terpenoid metabolism	High score 10	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104803.1:128079706-128083295 -	GO:0016102	Gene Card Expression Proteome JBrowse
`LXL04_026813` TK1151: - OH-1004: LXL04_026813	Terpenoid metabolism Terpenoid metabolism	High score 10	GOExpressionLocalizationPfamSwiss-Prot	CM104804.1:3335683-3337066 +	GO:0016102	Gene Card Expression Proteome JBrowse
`LXL04_028330` TK1151: - OH-1004: LXL04_028330	Latex/root related candidates Latex/root associated candidates	High score 10	GOExpressionLocalizationSwiss-Prot	CM104804.1:38172986-38179142 -	go:0010015 root morphogenesis biological_process	Gene Card Expression Proteome JBrowse
`TkA06G010180` TK1151: TkA06G010180;TkA07G328320 OH-1004: LXL04_029609	Latex/root related candidates Latex/root associated candidates	High score 10	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104804.1:95343079-95346257 -	go:0006970 response to osmotic stress biological_process	Gene Card Expression Proteome JBrowse

`TkA06G097970`

Terpenoid metabolismTerpenoid metabolismHigh · score 10

Source IDTkA06G097970

LocationCM104803.1:101545925-101547031 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0006720

Gene Card Expression Proteome JBrowse

`TkA06G091990`

MVA/MEP and isoprenoidPrenyl-donor metabolismHigh · score 10

Source IDTkA06G091990

LocationCM104803.1:103227375-103228292 -

EvidenceFunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidencego:0009824 amp dimethylallyltransferase activity molecular_function

Gene Card Expression Proteome JBrowse

`TkA06G086050`

MVA/MEP and isoprenoidMevalonate pathwayHigh · score 10

Source IDTkA06G086050

LocationCM104803.1:104470277-104471758 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0008299

Gene Card Expression Proteome JBrowse

`TkA06G047290`

Latex/root related candidatesLatex/root associated candidatesHigh · score 10

Source IDTkA06G047290

LocationCM104803.1:114805690-114807057 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidencego:0006950 response to stress biological_process

Gene Card Expression Proteome JBrowse

`TkA06G029790`

MVA/MEP and isoprenoidMevalonate pathwayHigh · score 10

Source IDTkA06G029790

LocationCM104803.1:120151407-120153739 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0008299

Gene Card Expression Proteome JBrowse

`TkA06G008820`

MVA/MEP and isoprenoidMevalonate pathwayHigh · score 10

Source IDTkA06G008820

LocationCM104803.1:127347496-127350406 +

EvidenceFunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidencego:0004421 hydroxymethylglutaryl-coa synthase activity molecular_function

Gene Card Expression Proteome JBrowse

`TkA04G085780`

Terpenoid metabolismTerpenoid metabolismHigh · score 10

Source IDTkA04G085780;TkA06G005680

LocationCM104803.1:128079706-128083295 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0016102

Gene Card Expression Proteome JBrowse

`LXL04_026813`

Terpenoid metabolismTerpenoid metabolismHigh · score 10

Source ID-

LocationCM104804.1:3335683-3337066 +

EvidenceGOExpressionLocalizationPfamSwiss-Prot

Key evidenceGO:0016102

Gene Card Expression Proteome JBrowse

`LXL04_028330`

Latex/root related candidatesLatex/root associated candidatesHigh · score 10

Source ID-

LocationCM104804.1:38172986-38179142 -

EvidenceGOExpressionLocalizationSwiss-Prot

Key evidencego:0010015 root morphogenesis biological_process

Gene Card Expression Proteome JBrowse

`TkA06G010180`

Latex/root related candidatesLatex/root associated candidatesHigh · score 10

Source IDTkA06G010180;TkA07G328320

LocationCM104804.1:95343079-95346257 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidencego:0006970 response to osmotic stress biological_process

Gene Card Expression Proteome JBrowse

Evidence Boundary

Current results integrate annotation, GO/KEGG, homology, predicted localization, domains, expression/proteome and network evidence. High/Medium/Low indicates evidence density and consistency, not experimental validation.