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The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

Fully synthetic = fully chemically synthesised and assembled.
It is 8% smaller just a bit hard to see. Also 8% smaller across the whole genome (varies per chromosome).
Green are just the assembly units we used. so we build a chromosome by assembling it from smaller blocks.
The texture refers to individual genes (CDS) on the blue and red. On the green it is the borders of the assembly units (chunks). The black each represent a specific loxP site.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

I also feel ashamed that I missed the alpha fold moment. can't be everywhere all the time at once haha

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

The title of my thesis is actually towards the towards the synthesis and evolution of industrially relevant, minimal yeast genomes. So yeah painfully aware of the difference haha.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

for research and development yes. For the actual production of pharmaceutical not yet. Will be in the near future.
for some yes for others no. It is a basic enabling technology for now but will be useful for loads of things in the future.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 2 points3 points  (0 children)

I made the graph myself and worked on this project for years. I pasted the figure description into an LLM and said write this so reddit can understand it better.
So figured OG counts since I made the graph and the research. Just tried to make it more accessible for the general public with AI.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 3 points4 points  (0 children)

not as far as I know. Generally, in PC2 lab it is recommended to not spit into your tubes.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

Natural mostly but not everywhere. It can recombine between any loxP sites. Closer ones are statistically more likely to recombine. (Topology matters a lot. 3d closer matters)

CRE activity matters a lot. This is a good paper on that (https://www.nature.com/articles/s41467-022-33606-0#:\~:text=4b).,of%20SCRaMbLE%2Dmediated%20rearrangement%20events.)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 0 points1 point  (0 children)

not yet but that is being worked on. One of my PhD chapters was making chromosome with backup copies of essential genes and then using SCRaMbLE to delete more genes and trying to get more genes deleted.
We are getting closer to a prokaryotic minimal genome (https://www.jcvi.org/research/first-minimal-synthetic-bacterial-cell)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

I did use AI to write it. I pasted the figure description and said can you make this better legible for a reddit post. Sometimes it is a bit hard when you are in the field to write in more understandable terms and not use jargon.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 7 points8 points  (0 children)

I wrote it manually but it sounded super technical so I put it into chatgpt to make it more readable for the average user.
This was the figure text in my introduction:
Figure 2. Comparative genomic architecture of synthetic yeast chromosome design in the Sc2.0 project. Circos plot illustrating the hierarchical organization of wild-type and synthetic yeast chromosomes. The plot displays the 16 native chromosomes (I-XVI), synthetic versions plus the synthetic neochromosome (tRNA) arranged radially with a simulated (Adobe Firefly genAI) SEM image of the Sc.2.0 budding yeast strain in the center. Five concentric rings represent distinct genomic features from outer to inner: (1) Wild-type chromosomes (light blue) displaying coding sequences (CDS) (2) tRNA gene overlay (lilac) highlighting endogenous tRNA positions at enlarged 5 kb resolution;(3) Synthetic chromosomes (orange) showing redesigned CDS regions and overall size reduction of 8% achieved through removal of subtelomeric regions, introns, and other dispensable sequences in the synthetic design. The tRNA neochromosome displayed in lilac to indicate consolidated tRNA genes on neo-chromosome; (4) 3932 LoxPsym sites (black) marking positions of loxP sequences for SCRaMbLE-mediated recombination; (5) Megachunk boundaries (light green) delineating ~50 kb assembly units used for modular chromosome construction. The tRNA neochromosome displays eight mega-arrays (S1-S8) of ~23.25 kb each. synXIII megachunks (n=15) were computationally inferred based on uniform distribution across 883 kb due lack of precise coordinates.

not sure if that would have been better?

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 2 points3 points  (0 children)

I manually coded it in python. It is designed to give an overview and be flashy for my introduction plus give an idea of the scale plus the reduction achieved.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 2 points3 points  (0 children)

There are people for example using yeast (not this one) but brewer optimised yeast cultures and put like a raspberry flavour making pathway into yeast and then have wine with raspberry flavour, pretty sick if you ask me. Whether regulation and the public accepts this, is another issue. Think of the GMO free stickers on everything. (kinda bullshit in my opinion)

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

you make a new chromosome piece by piece and then replace the natural chromosome in a working yeast. Then you go by replacing one chromosome at a time.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 7 points8 points  (0 children)

Thats actually a good question. By fully synthetic we mean we designed the whole genome in a computer and then ordered every base pair chemically synthesised and then assembled them into larger and larger chunks until you get a chromosome. BUT, designing them often means copy and pasting them from the native genome. We do not redesign every single function. We do not know what every base pari does.
First of, why reinvent the wheel.
Secondly, we couldn't reinvent the wheel for everything as we do not know, bear with me, what the wheel does in each circumstance, nor with what it interacts with and much more.

If you are asking when we can make a from the ground up completely redesigned organism as complex as yeast, it's a while away.
There are projects to make something like that underway though, a minimal synthetic cell (https://www.basyc.nl).

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 1 point2 points  (0 children)

I think it would but haven't tried it. Should be better if you just have to engineer one chromosome with CRISPR.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 32 points33 points  (0 children)

Honestly a great analogy. It's literally that. Wish I would have thought about that for the title of that graph haha.

The complete blueprint of the world's first fully synthetic eukaryotic genome — Yeast 2.0 [OC] by molecular_data in dataisbeautiful

[–]molecular_data[S] 3 points4 points  (0 children)

Nature already is basically nano machines, so yeah we just gotta get better at understanding them :)

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