**Rhynchospora tenuis+++++

This plant belongs to the Cyperaceae family. It has a haploid set of chromosomes of two (n=2), the lowest chromosome number in the entire higher plant kingdom. This species is native to Central and South America. It is not currently involved in any evolutionary disputes; rather, it exists with no significant selection pressures. Understanding this plant is crucial for comparing its typical genes and traits with those of regular plants.
Our goal is to randomly select several genes and key factors for study. Ultimately, we aim to understand the structure of intron co-acting and intergenic sequences and their typical state when not immediately active.
The choice of this plant species is motivated by several factors: it has only two chromosomes, PacBio sequencing quality is exceptionally high, NCBI provides the necessary tools for online research and analysis, and this species receives limited attention within the scientific community.
Note that the general validity of this investigation for other plants is limited to the PacBio SMRT (Sequel II) system or similar techniques.

It is a high-throughput DNA sequencing instrument developed by Pacific Biosciences that uses Single Molecule, Real-Time (SMRT) sequencing technology to generate highly accurate long reads with high precision and speed. Released in 2019, the Sequel II system significantly increased data output and reduced costs compared to previous versions, making comprehensive genomic and transcriptomic analysis more accessible for various life science applications, such as de novo genome assembly and variant detection.

1)  R2R3 WEREWOLF like MYB ortholog: AT5G14750; ID: gene-LUZ61_017606

Werewolf influences the root hair growth and is also involved in the flowering time.

The MYB "WEREWOLF" region on Chromosome 2 consists of three coding exons (1-3) and two introns (1-2). In intron 2, there may be a stem-loop-stem hairpin structure that generally co-activates the production of MYB proteins.

In the next step, we will compare (blast) the DNA sequence (highlighted in red) with R. tenuis PacBio HiFi sequencing, which includes over 800,000 extended-read sequences.
The graphical distribution aligns with our expectations. The results from the first 30 hits appear uniform, indicating that we examined a 2000-base window from 30 different cells of the same plant individual. Still, we did not identify a single somatic mutation. This also suggests that the plant is homozygous for this MYB gene.

We have presented here the simplest case one can encounter. We achieve very high sequencing accuracy, unlike this method some years ago.
We will proceed to a more complex case in the hope of gaining further insight into these molecular regulating processes.

Sections 2 and 3 deal with ANS. 

The ANS protein, or anthocyanidin synthase, is a key enzyme in the plant's anthocyanin biosynthesis pathway that catalyzes the final step in producing colored anthocyanidins. Specifically, it converts colorless leucoanthocyanidins into colored anthocyanidins, which then form anthocyanins (the final plant pigments) by attaching to sugar molecules. This enzyme is crucial for flower and fruit color, for attracting pollinators and seed dispersers, and for contributing to plant stress resistance.

This enzyme can be found on Chromosome 1. It also has three coding regions and two introns.

This individual has two haplotype formations at identical loci. We observe that 50% of the haplotypes are haplotype A and 50% are haplotype a. The graph clearly illustrates the exons and introns.

Interestingly, there is almost no noticeable difference in the coding regions (exons) between the two haplotypes. In contrast, the introns show significant differences in their coding, suggesting they may play a role in gene regulation.

Section 3

We turn our attention back to the enzyme ANS located on Chromosome 1. This time, we will closely examine intron 1, where we observe a repeating poly (T) sequence. In haplotype (a), the length of T repeats is ten in each of the 11 long reads. Among these 11 haplotype strings (A), we count five instances of 15 T repeats and six of 16 T repeats. We have found this feature in several different plant species. It’s common to see one additional repeat at the beginning or end of the short tandem repeat (STR) reading direction. This variation cannot be attributed to sequencing errors or inaccuracies in the copying machinery; it might suggest a different underlying process. We will revisit somatic mutations later.

4) Antiporter (DRAFT)

from (KI)

An antiporter in plants is a type of membrane transport protein, not an enzyme, that moves two different molecules or ions in opposite directions across a membrane. It uses the energy from one molecule moving down its concentration gradient to power the movement of another molecule against its gradient. A key example in plants is the Na+/H+ antiporter (NHX), which plays a crucial role in salt tolerance by transporting sodium ions out of the cytoplasm into the vacuole and by regulating pH and ion homeostasis.

Somatic mutations occur at the ends of poly(N) strings during each cell division (mitosis, somatic mosaicism). As a result, no two cell genomes within a plant's tissue are identical. Despite these variations, the tissue's structural integrity remains intact due to a subtle burst of energy and information emanating from the microcosm. Some refer to this phenomenon as quantum mechanics.
Additionally, consider the examples of short tandem repeats (STRs) such as poly(TA) and poly(C), which can vary in length from cell to cell within the same individual's tissue (∆TA, ∆A, ∆G, ∆C).

5)

With ribosomal DNA (rDNA), we show another feature that will convince you that quantum events, rather than classical ones, drive the plant world.

Ribosomal DNA (rDNA) is the section of a genome that codes for ribosomal RNA (rRNA), which is a crucial component of ribosomes and essential for protein synthesis. These DNA sequences are found in all organisms and are often repeated many times to meet the high demand for ribosomes in the cell.

On Chromosome 1, the identical rDNA is repeated exactly 682 times. The difference is that the poly(A) STRs vary in length.

On SRX13424990, one can find the string (A) of 50 different cells. From this, we aim to make a movie that models what happens to the poly(A) tails each time a cell is about to divide.

We are modeling the lengths of poly(A) tails for six rDNA sequences across 13 different cells of the same individual plant. The positions of the six rDNAs are consistent in each case, allowing us to examine how each cell can independently adjust the length of the poly(A) tail. If this length correlates with any co-activating mechanisms, it could have significant implications for how living organisms behave in relation to the principles of quantum mechanics.

The second version discusses the rDNA length of poly(A) STRs from 50 cells at the same locus (A) in SRX13424990. This somatic variation in rDNA STRs is extremely high, making it one of the most variable loci found in any genome. (Soundtrack: Hot Butter Popcorn instrumental) locus A: CHR1, CM05888.1: 104,420,020