Antirrhinum striatum/pseudomajus

Upon examining the two most recent papers on A. pseudomajus and A. striatum, it becomes evident that the authors 1_2 * describe a regulatory network in the context of molecular genetics. This network encompasses not only individual organisms but also entire populations and their interactions with both biotic and abiotic environments. *The genomic plant material was collected in 2010, 2107-2019. We have read 3, 4, 5, 6.

The results are both new and exciting for us. We appreciate the asymmetric stepped clines produced by the six floral pigments, as well as the underlying MYB factors and other influences. However, we believe there is a more logical explanation than the notion that marathon bumblebees are flying from both ends of the subspecies ranges into the mixed zone, which aligns with the authors' expectations. Furthermore, the populations are already gradually intermixing across the entire range, incorporating genes from both subspecies. As a result, the idea of hybridization has only weak support. Upon inspecting all the molecular markers that the authors have used over the years, we concluded that the red markers are rarely present in yellow plants. We observed some plant-inhabiting retrotransposons and non-coding RNAs near the pigment-activating MYBs, which suggests that an undiscovered but highly sophisticated mechanism can transform a yellow flowering plant into a red one.

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*They state, «There are no obvious differences in the physical environment or pollinators in the transition of yellow and magenta flowered populations.»
In addition, a clinal transition between the populations with different flower coloration is postulated. The flowers themselves also show gradual pigment differences from proximal to distal in the petals.
The text focuses on the accurate formation of molecular gradients that have no apparent connection to natural selection. However, in (3), the authors attempt to explain it in terms of mutation-selection, which is not at all convincing to us. They do not investigate the molecular factors underlying the process or its fine-tuning characteristics.

These findings are interesting in that they warrant further examination of the regulatory networks and gradient formation in the petals, as well as the steep clines in allele frequencies across the transitional zone.

However, without a well-annotated genome of A. pseudomajus published at https://www.ncbi.nlm.nih.gov/, long- and deep-read sequencing (SMRT), and objective color measurement using a handheld color spectrometer, there will be no substantial improvement in this field in the near future. It will be sufficient to analyze both end stages (striatum & pseudomajus) and about four stages in between to obtain good results.

It is vital to sample fresh petal material  (no reproduction tissue nor pollen) for a SMRT long and deep read for WGS. One hundred repeats would be sufficient. It is best to use DNA extraction from seeds of wild plants propagated in a greenhouse. RNA_seq is already available; there is no need for further investigation. The group has sampled and analyzed hundreds, if not more, individuals, but the most published data on nih.gov dates back 15 years. The published data set for 2017-19 has previously been filtered and lacks the most interesting data points.

We also reviewed Hugo Tavares's PhD thesis (2014). He suggests that the hybrid zone might be approximately 100 years old, and that the variation between the R1 and r1 loci could be found in some introns of the corresponding genes.

A)

We have drawn a substitute circuit diagram (model presentation) that can plausibly account for all molecular genetic conditions associated with ROS1. Since the exons of ROS1 (1-3) do not differ in the two subspecies A.m. pseudomajus and A.m. striatum, it is evident that the repetitive sequence located in the intron (STR) can play a decisive role in the activity of the MYB. There are two varieties of repetition: either poly TAA in A. pseudomajus or poly TTA in striatum. Above STR in the picture, one will find an internal slider, which, depending on its two extreme positions, either induces uniform sequences or does not, if the triplets are all TAA, resulting in a dominant factor of ROS1. If all triplets are of the structure TTA, the recessive factor is the result (ros1). The MYB factor is then not active. Heterogeneous triplets also occur, which means that the slider occupies a middle position. Even with a hybridization of both forms, this system can also influence the gene activity at this position in F1 and F2 plants.  

Location of the TAA-string of ROS1 on chromosome 6  

The intron strings should always show poly TAA for magenta red pseudomajus or poly TTA for yellow striatum flowers, even when you have a mixture of genomic haploid material from 50 plants. MP4 falls at the red end of the hybrid zone, seen around 2013. Surprisingly, some strings displayed a chimeric form of yellow and red strings, namely: TAATAATAATATTATTATTATTATAATAATAATAATAATAA. The latter highlights a molecular mechanism that influences the activity of the Myb factor ROS1. This mechanism can transform the yellow string into a red string, activating the previously inactive ROS1_Myb factor.

In Antirrhinum hispanicum, with its pale violet flowers, the STR within the ROS1 intron is represented as follows: (TTATTATTATTATTATTATTATTATTATTATAATAAT). This suggests that this STR influences MYB gene activity and color density.
In this case, the ROS-MYB is nearly downregulated, resulting in a whitish violet color. (+ EL, SULF)

B) There are more sliders!

The circuit diagram, along with the Fst divergence from Tavares (2014), illustrates the data. The extreme points of the graph correspond to the Short Tandem Repeats (STRs) for ROS1_2 and EL. In the substitute circuit diagram below, the three sliders create a magenta-red flower. By slightly adjusting the lengths of the STR strings, it is possible to achieve every conceivable combination. The lowest extremes are ros1, ros2, and EL, which can be fine-tuned using the yellow flowers. The slider regulator is a theoretical addition designed to facilitate this adjustment (rheostat or tuning knob).
These findings reveal a more advanced opportunity to uncover the most effective factors for modifying floral shape and color in the Catalan Snapdragon.

 Another slider is seen on Chromosome 2. In the intron of the Retrotransposon COPIA, a very long  TATA STR is seen. The TATA string is very long in pure Antirrhinum pseudomajus, but shorter in A. striatum. The active TE can influence the expression level of neighboring genes and slightly alter the genomic information.

On Chromosome 4, the SULF locus is located in the striatum (Y) and pseudomajus (M), which is genomically richer in the yellow subspecies. The red colored portions 1) and 2) are not missing in the striatum subspecies, far away from a hybrid (transition) zone. SULF has a 4'CGT sequence (light green), a binding sequence*, followed by a reverse-complement 4'CGT sequence (light blue). At least one RNA string of this sequence can form a double-stranded RNA with any 4'CGT RNA. In subspecies pseudomajus, this Gene is fully expressed (on the right),  (SRX27905825 RNA_seq psdms)

, *transposon insertion site

But in the striatum, the gene is partially expressed (on the right) and therefore nonfunctional. This effect may be due to the central transposon-like string. In some striatum subspecies, particularly in the western part of the hybrid zone, the red portion 1) is absent. It appears that the SULF gene can spontaneously switch between the SULF and sulf allelic forms, depending on the adapting needs.

    (SRX27905828 RNA_seq striatum)

 A fully expressed SULF can downregulate the aurone synthesis. Note that near SULF, a protein kinase is located, which serves cell-to-cell communication. 

A factor on chromosome 8 is necessary for making the veins of the upper lobe anthocyanin-colored when active, as shown in the upper picture. Also, this MYB has a slider. The end positions VE and ve are seen mostly outside the transition ("hybrid") zone. Intermediated states can be encountered within the zone. The transition from one state to another is primarily brought about by these sliders, mainly within the transition zone, through internal regulation. This process can begin quickly when a threshold mark is reached.

 A long STR of polyA corresponds to clearly visible dark veins, whereas shorter strings lead to less prominent or, when too short, no dark veins. The end states ve and VE, as well as the intermediate states, are heritable in a Mendelian manner.

In the long run, striatum individuals alter their cues towards a pseudomajus shape, which is thermodynamically the better fit and brings about greater stability in the suddenly warmer climate in these upper hills. The so-called "hybrid zone" is expected to fade out in the coming years.
It is relatively easy for them (the striatum subspecies plant individuals) to fulfill their role; they possess internal molecular genetic mechanisms (such as sliders and switches) that can perform the task. More details coming up later on.

Additional notes:

Subspecies pseudomajus and striatum are both biennial plants. In 2020, Plant #17 had dark magenta upper lobes, while in 2021, the color changed to purplish red. During the same period, the base color of the flower shifted from reddish violet to bluish violet. Additionally, the flower in 2021 expressed less yellow aurone pigment compared to the previous year. This suggests that the expression of pigments in flowers within the "hybrid zone" may change over time in the somatic tissue. If the progressively changing RNA status can be traced back to genomic information, it could indicate a steady rate of floral evolution in this so-called hybrid zone.

There is a noticeable increase in anthocyanin pigments in apical buds and petioles before the change in floral pigments.

The individual plants are developing a new floral shape, including color, and must also undergo genetic updates to ensure safety for future generations.

 (1) The process of Snapdragon evolution might be rapid. The so-called hybrid zone is believed to be no more than 100 years old.

2) Introns are non-coding regions of DNA found within genes of A. majus genomes, especially in MYB factors. They can contain regulatory elements that control gene expression (including enhancers and silencers) and the splicing process. We primarily focus on Short Tandem Repeats (STRs) in the context of regulatory elements.

3) Firstly, the coding sequences of genes such as MYB-ROS1 remain unchanged between the subspecies pseudomajus and striatum; however, the length of the short tandem repeats (STRs) does vary. Secondly, the dominant or recessive traits of these alleles are likely influenced by the length of the STRs, which affects the transcription process of MYB-ROS1.
4) The entire process of evolution is driven by an autoregulatory network of various regulatory genes that can sometimes speed up after reaching the threshold limit. It is a so-called emergent property. See Cell 2022 Chapter 2, p.49.

 5) It seems that these living systems can "learn" to adapt to the new circumstances. The new fit is then registered in the genome simply by the elongation or shortening of STRs in several introns. This phenomenon has been observed in two different taxa: Diplacus puniceus and Antirrhinum majus.

It is becoming increasingly clear that the evolution of biological structures does not rely solely on random mutations or natural selection. Instead, these structures have established norms and mechanisms that allow them to make significant adjustments when necessary, and these changes are maintained over time.

From now on, please conduct genomic analyses using a PacBio HiFi instrument, which enables long DNA reads with exceptional accuracy.  Alternatively, you can perform single-cell genomic analysis on the tissue of a single flower bud from the plant in question. This approach enables you to detect the haplotype quotient and determine whether short tandem repeats (STRs) vary within a single plant.

rolfy October 24, 2025

See also The Pushmi-Pullyu-Code