R2R3MYB2 Transcription Factor SRX6077453 JX661264.1
This anthocyanin transcription activator gene is present by default in every Diplacus plant. Several motifs in the introns and exons should have appropriate length and information unless the activator is not fully upregulated. These include the promoter, the TATA motif, the Tctctata motif, and the ear motif 6AB.
Orange-flowered Diplacus plants (T30, Potrero 9.1) lack one or more of these motifs, or the TATA motifs are too short. Yellow-flowered species lack all these motifs, and all the TATA motifs tend to be short. All these motifs are thought to be altered by autoregulation within the plant's individuals, and to a lesser extent by hybridization and backcrossing.
See: Mimulus aurantiacus ecotype Red putative R2R3 MYB transcriptional regulator (Myb2) gene, complete cds Sequence ID: JX661264.1 Look up for this typical (...tctctctata...) string!
In reality, there are more spots. Along this TF, we revealed six regulatory sites. Biased or directed somatic mutations can occur, resulting in a regulatory change affecting the floral color. The autoregulation of these specific sites will help fine-tune any "hybrid" state. Generally, it forms a genuinely red flower. - Few other enzymes or transcriptional factors are prone to having a very similar mechanism in Diplacus varieties (DFR, Protein Kinase, MaMyb1, MYB4, F3H, GST, Limonene Synthase, ANS, Anthocyanin Repressor).
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Functional elements within introns or in exon 3 of MaMyb1
TATA-Box: On-Off-Switch
6B-motif: Activator of MYB-TF activity
STRs: Enhancer-Strings
SPI: Different Splicing Manner
Terminator: not evaluated
*Truth Table/Algorithm (valid for all Diplacus aurantiacus varieties)
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No Promoter, no Ear-motif --> YELLOW FLOWER
No Promoter, no Ear-motif but long STRs --> light ORANGE flower
With Promotor and Ear-motif but very short STRs --> YELLOW Flower
With Promotor and Ear-motif and medium-sized STRs --> DARK ORANGE flower
With Promotor and Ear-motif and well-sized STRs --> ordinary RED flower color
SPI: three different types of splicing; affects the Hue of the flower color (from cardinal red to dark magenta)
(based on theoretical assumptions; AI-like approach)*
SRX6077409 PUN-LH19-2016 33.0609, -117.1188
D. puniceus
ear motif: yes
STR 2nd intron CTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATATATAT±
TATA length varies from individual to individual (15-24 TAs)
with an ear motif, long hairpin
anthocyanin activating R2R3MYB2 is upregulated -> red flowers
D. ana hairpin?/EM?
The hairpin should be extended with an ear motif. The Subspecies has been in Statu Nascendi since 2010. More genomic background is needed in this case.
RUT_WTF (SRX19694291) 34.2174, -117.7630
Diplacus rutilus (longiflorus subspecies)
ear motif: GAAATGAGT
STR in 2nd intron:
TCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATATATATATATATAT
hairpin: long
ear motif & long hairpin -->
Anthocyanin activating R2R3MYB2 is upregulated ->
dark red floral color
PAR-KK182 SRX6077455 34.0193, -119.6802 East of Prisoners Harbor
D. parviflorus
ear motif: yes
in 2nd intron: hairpin with two stems and loop GTTAAAT
self-complementary hairpin
GCCTAAAACTCTATCTGCCTGTCTATATATCTCGTTAAATGATATATAGACAGGCAGATAGAGTTTTAGGT
or with an inverse loop:
GCCTAAAACTCTATCTGCCTGTCTATATATCATTTAACGAGATATATAGACAGGCAGATAGAGTTTTAGGT
This kind of complementary hairpin is unique for the red Diplacus found on Santa Cruz Island. We would like to know if plants growing on the neighbouring Anacapa and Santa Rosa Islands have similar hairpins.
Anthocyanin activating R2R3MYB2 is upregulated ->
darker red floral color
Stem-LOOP-Stem hairpin
Note: Only the Channel Islands Diplacus parviflorus has this kind of hairpin.
Diplacus longiflorus on Santa Cruz Island has a TATA hairpin.
cf.
33.354895, -118.350723 Santa Catalina Island
Diplacus "catalina"
This Diplacus plant belongs to a separate variety. It is not a Diplacus parviflora. Here, some genomic analyses should also be done to clarify its status.
We expect an EAR motif here and long STRs in the first and second introns of the R2R3MYB2-Tf.
*****
We have yet to succeed in extending genomic studies in plants in transition. We aim to conduct these studies to gain insight into this transition's molecular mechanism.
We mention what we have so far:
After cultivating an offspring of two yellow-flowered D. australis plants,
We received a light orange-flowered plant instead of the yellow one we ordered. It is not an actual F1 plant. In the IGV (Integrative Genomics Viewer), we could identify a longer TATA string and an EAR motif in some sequences. Neither did we expect. Some spontaneous alterations occurred during propagation and cell division, which is what we followed.
Somatic mutations of Potrero_9-1-cult
To enlarge, click on the pic.
This plant individual, a cultivated cutting from a Potrero yellow wild plant, has spontaneously enlarged the polyA STR and shortened its polyTA STR at the same time.
An F1-plant would not have such a pattern. Consequently, the flowers turned to a light orange hue.
- *****
SRX6077154 AUR-T92_6 37.8459, -120.6110 East of Oakdale
D. aurantiacus
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATTTATATATATATATATAT±
no ear motif, long hairpin --> activates aurone only
Anthocyanin activating R2R3MYB2 is downregulated -> golden yellow flowers
SRX6077462 LON-33_1 34.3438, -118.5099
San Fernando Pass Race D. longiflorus golden yellow
ear motif: no
STR in second intron:
TCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATAT
no ear motif, long hairpin --> activates aurone only
Anthocyanin activating R2R3MYB2 is downregulated -> golden yellow flowers
SRX6077459 LON-T8_8 34.1347, -118.6452 Santa Monica Mts.
D. longiflorus
TCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATAT±
no ear motif, short hairpin -->
Anthocyanin activating R2R3MYB2 is downregulated -> pale color to deep yellow;
SRX6077244 CAL-T90_2 35.5918, -118.5052 near Lake Isabella
D. calycinus
ear motif: no CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATATATATATATAT
no ear motif, short hairpin -->
Anthocyanin activating R2R3MYB2 is downregulated -> yellow color
SRX6077239 GRA-T101_10 39.5536, -121.4301
grandiflorus
CTCTCTCTCTCTCTCTCTTAAATGATATATA
(pic from the internet)
no ear motif, not a valid hairpin sequence -->
Anthocyanin-activating R2R3MYB2 is downregulated, resulting in a yellow color.
SRX6077405 PUN-POTR15-2016 32.6038, -116.6339 W of Potrero
D. australis
ear motif: no
CTCTCTCTCTCTATATATATATATATATA±
no ear motif; shorter hairpin
anthocyanin activating R2R3MYB2 is downregulated -> salmon yellow to deep yellow flwrs
SRX6077155 ARI-159 32.6630, -116.2230 near Iron Spring
D. aridus
ear motif: yes
CTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATAT
ear motif; short hairpin
anthocyanin activating R2R3MYB2 is downregulated -> pale yellow flowers
28.346337, -115.209025 Cedros Island, Baja California
D. stellata.
We expect no ear motif and short or no hairpin here.
Genomic information needed.
herbarium specimen
SRX6077240 33.1589, -116.8122
D. clevelandii
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATAT±
no ear motif; short hairpin
anthocyanin activating R2R3MYB2 is downregulated -> yellow flowers to deep yellow flowers
The result is strikingly different from what is expected. The coding region (ex2) remains unchanged across all diplacus varieties. On the contrary, in both introns,
A lot of pushmi-pullyu code (TATA) makes the difference.
In an evolutionary context, what is written in introns is more important than what is in exons and not vice versa.
See the TATA-language for amusement.
https://www.youtube.com/watch?v=_JmA2ClUvU
*Such STRs in introns are not unique to Diplacus. They occur more frequently in autonomous regulating proteins in all plants.
Occurrence of Short Tandem Repeats in introns throughout the plant kingdom. 350 Taxa. Unpublished study (Schmid/Baumberger 2023)
Note: Biased TATA-String changes bring about phenotypic changes up to 10,000 times faster than the scientific community might expect from the outcome of Darwinian Evolution.
MW Schmid and I, Rolf Baumberger, were preparing a publication on the topic of short tandem repeats as regulatory elements in the introns of plants.
09-12-2025 rolfy