Abstract
Lithospermum erythrorhizon is a medicinal plant valued for its ability to produce shikonin and its derivatives, a compound with important pharmacological properties. While R2R3-MYB transcription factors are known regulators of plant metabolism, no genome-wide analysis had been conducted in L. erythrorhizon. In this study, we present the comprehensive identification and evolutionary study of R2R3-MYBs in L. erythrorhizon, characterizing 176 LeMYB genes. Structural and conserved motif analyses revealed that the R2 and R3 domains of LeMYBs are relatively conserved, while sequence diversity has progressively emerged during evolution. Phylogenetic analysis classified the LeMYBs into 31 subfamilies, expanded mainly through whole-genome duplication, transposed duplication, and dispersed duplication. Expression profiling identified that certain LeMYBs exhibit root/leaf/flower-specific expression, with LeMYB1 predominantly expressed in roots, showing a 63-fold increase in transcript levels compared to leaves and significant upregulation under shikonin-inducing conditions. Subcellular localization confirmed that LeMYB1 is a nucleus-localized protein. Finally, yeast one-hybrid (Y1H) and dual-luciferase reporter assays collectively demonstrate that LeMYB1 binds to the promoters of key shikonin biosynthetic enzyme genes (LeHMGR2, LeGPPS1, LePGT1, LeGHQ3''H2, and LeSAT1) and activates their transcription, thereby promoting shikonin biosynthesis. This study provides the first genome-wide evolutionary analysis of R2R3-MYBs in L. erythrorhizon and reveals that LeMYB1 coordinately regulates multiple shikonin biosynthetic genes, laying the foundation for elucidating the regulatory mechanisms of shikonin biosynthesis and for mining potential transcription factors for genetic improvement.
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Claims 15
Claim · model-written summary
The study identified 176 LeMYB genes.
- Taxon
- Lithospermum erythrorhizon
Lithospermum erythrorhizont0 - Gene
- LeMYBe1
- Outcome
- LeMYB genese1
- Value
- 176e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“characterizing 176 LeMYB genes”
Claim · model-written summary
The R2 and R3 domains of LeMYBs were relatively conserved.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYBse1
- Outcome
- R2 and R3 domains of LeMYBs are relatively conservede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“the R2 and R3 domains of LeMYBs are relatively conserved”
Claim · model-written summary
LeMYB sequence diversity emerged progressively during evolution.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Outcome
- sequence diversity has progressively emergede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“sequence diversity has progressively emerged during evolution”
Claim · model-written summary
Phylogenetic analysis classified LeMYBs into 31 subfamilies.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYBse1
- Outcome
- subfamiliese1
- Value
- 31e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“Phylogenetic analysis classified the LeMYBs into 31 subfamilies”
Claim · model-written summary
Whole-genome duplication mainly expanded the LeMYB subfamilies.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Outcome
- expandede1
- Qualifier
- whole-genome duplicatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“expanded mainly through whole-genome duplication, transposed duplication, and dispersed duplication”
Claim · model-written summary
Transposed duplication mainly expanded the LeMYB subfamilies.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Outcome
- expandede1
- Qualifier
- transposed duplicatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“expanded mainly through whole-genome duplication, transposed duplication, and dispersed duplication”
Claim · model-written summary
Dispersed duplication mainly expanded the LeMYB subfamilies.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Outcome
- expandede1
- Qualifier
- dispersed duplicatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“expanded mainly through whole-genome duplication, transposed duplication, and dispersed duplication”
Claim · model-written summary
Some LeMYBs had root, leaf or flower-specific expression.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYBse1
- Outcome
- root/leaf/flower-specific expressione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“certain LeMYBs exhibit root/leaf/flower-specific expression”
Claim · model-written summary
LeMYB1 transcript levels were 63-fold higher in roots than leaves.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Organ / stage
- rootse1
- Gene
- LeMYB1e1
- Outcome
- transcript levelse1
- Direction
- increasee1
- Value
- 63-folde1
- Comparator
- leavese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“LeMYB1 predominantly expressed in roots, showing a 63-fold increase in transcript levels compared to leaves”
Claim · model-written summary
Shikonin-inducing conditions significantly upregulated LeMYB1.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Treatment
- shikonin-inducing conditionse1
- Gene
- LeMYB1e0
- Outcome
- upregulatione1
- Direction
- upregulatione1
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e0“LeMYB1 predominantly expressed in roots, showing a 63-fold increase in transcript levels compared to leaves”
e1“significant upregulation under shikonin-inducing conditions”
Claim · model-written summary
LeMYB1 was localized in the nucleus.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYB1e1
- Outcome
- nucleus-localized proteine1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“LeMYB1 is a nucleus-localized protein”
Claim · model-written summary
LeMYB1 bound promoters of LeHMGR2, LeGPPS1 and LePGT1.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYB1e1
- Outcome
- binds to the promoters of key shikonin biosynthetic enzyme genese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“LeMYB1 binds to the promoters of key shikonin biosynthetic enzyme genes (LeHMGR2, LeGPPS1, LePGT1, LeGHQ3''H2, and LeSAT1)”
Claim · model-written summary
LeMYB1 bound promoters of LeGHQ3''H2 and LeSAT1.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYB1e1
- Outcome
- binds to the promoters of key shikonin biosynthetic enzyme genese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“LeMYB1 binds to the promoters of key shikonin biosynthetic enzyme genes (LeHMGR2, LeGPPS1, LePGT1, LeGHQ3''H2, and LeSAT1)”
Claim · model-written summary
LeMYB1 activated transcription of the named shikonin biosynthetic genes.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Gene
- LeMYB1e1
- Outcome
- activates their transcriptione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“LeMYB1 binds to the promoters of key shikonin biosynthetic enzyme genes (LeHMGR2, LeGPPS1, LePGT1, LeGHQ3''H2, and LeSAT1) and activates their transcription”
Claim · model-written summary
LeMYB1 promoted shikonin biosynthesis through transcriptional activation.
- Taxon
- Lithospermum erythrorhizonLithospermum erythrorhizont0
- Outcome
- shikonin biosynthesise1
- Qualifier
- activates their transcriptione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Lithospermum erythrorhizon”
e1“activates their transcription, thereby promoting shikonin biosynthesis”