Transition studies 

 in plants             by Rolf Baumberger 

 Diplacus short tandem repeats* and "ear motif= GAAATGAGT" of all varieties in anthocyanin activating R2R3MYB2

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!

 

SRX6077409 PUN-LH19-2016           33.0609, -117.1188

D. puniceus

ear motif: yes
STR 2nd intron CTCTCTCTCTCTCTCTCTCTCTCTCTATATATATATATATATATATATATATATATATATAT±

TATA-length varies from individuum to individuum (15-24 TAs)

with ear motif, long hairpin
anthocyanin activating R2R3MYB2 is upregulated -> red flowers

                                                     33.659195, -117.449456 

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. parviflora

ear motif: yes

in 2nd intron: hairpin with two stems and loop GTTAAT

GCCTAAAACTCTATCTGCCTGTCTATATATCTCGTTAAATGATATATAGACAGGCAGATAGAGTTTTAGGT


Anthocyanin activating R2R3MYB2 is upregulated ->
darker red floral color

very long mRNA 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 motiv here and long STRs in the first and second intron of the R2R3MYB2-Tf.

*****

We have yet to succeed in extending genomic studies in plants in transition. We aim to fulfill 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 got a light orange-flowered plant instead of a yellow one. It is not a F1-plant.
In the IGV (integrated genome viewer), we could make out a longer TATA string and an ear motif in some strings. Both, we did not expect. Some spontaneous altering took place during propagation, and that is what we followed.

Potrero_9-1-cult

 

To enlarge click on the pic

*****

 

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 internet)

no ear motif, not a valid hairpin sequence   -->
Anthocyanin activating R2R3MYB2 is downregulated -> 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

 


 

Summary plot of MYB-TF in Diplacus

The result is strikingly different from what is expected. The coding region (ex2) does not change over 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.

 

https://www.youtube.com/watch?v=_JmA2ClUvUY

“TaTa-talking“!!!

*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)