Genome Foundations: Structure and Expression

Written by Kaskrim • Scribed by AI Elara • Project Gorgon Genetics Research

This article covers the foundational concepts that apply to all breedable species in Project Gorgon. The arthropod and horse genome structure articles build on this foundation — read this first.

For Mendelian genetics fundamentals (alleles, the six crosses, clarification, inbreeding), see Genetics Basics and Inbreeding.

The Genome Grid

Every specimen's genome is displayed as a grid in the genetics window. The grid is organized into chromosomes and gene groups.

Chromosomes (Rows)

Each row in the grid is a chromosome, numbered CR 1, CR 2, CR 3, and so on. The number of chromosomes differs by species. Arthropods have 10; horses have 48. Each chromosome controls one or more traits — color, body scale, glow, particle effects, stats, and more.

Gene Groups (Columns)

Each chromosome is divided into gene groups, labeled A through L (not all chromosomes use all columns). Each gene group contains up to 4 sub-positions, labeled 1 through 4. So a full gene group has positions 1, 2, 3, and 4. Not all gene groups are full — some chromosomes have shorter gene groups at the end.

Gene Positions

The smallest unit in the genome is a single gene position. Each position holds one gene — the three-state symbol you see in the genetics window (⬤, 〇, or ⦿). A gene position is referenced by its chromosome, gene group, and sub-position number.

Coordinate System

Breeders reference specific gene positions using a coordinate:

[Chromosome][Gene Group][Position]

Examples:

1A4  = Chromosome 1, Gene Group A, Position 4
9E4  = Chromosome 9, Gene Group E, Position 4
6C2  = Chromosome 6, Gene Group C, Position 2

This coordinate system is used across all breeding records, naming conventions, and community documentation. When a breeder says "I'm working on 3H3," they mean chromosome 3, gene group H, position 3.

How to Read the Genetics Window

The Three Symbols

Each gene position in the genetics window displays as one of four symbols:

• ⬤ Filled circle = Double Dominant — both alleles are dominant. This gene breeds true.
• 〇 Open circle = Double Recessive — both alleles are recessive. This gene breeds true. For arthropods, stat bonuses express here.
• ⦿ Circle with dot = Mixed — one dominant allele, one recessive allele. Unpredictable. This is what clarification works to eliminate.
• ? Question mark = Unknown — your Genetics skill is too low to read this position. Level up to reveal it.

Text Export

The game can also export a specimen's genome as a plain text file. The text export uses a different notation from the genetics window:

[Overview]
Format=v1.0
Character=PlayerName
Entity=Baby Fae Bee 2483
Genome=BeeWasp

[Genes]
01=  RRRR RxRR RRRx RRRD ...
02=  ...

Text export uses: D = ⬤ (dominant), R = 〇 (recessive), x = ⦿ (mixed), ? = unknown

These are two distinct formats — the genetics window and the text export use different symbols for the same information.

Decode Types

Note: The examples used throughout this section are drawn from arthropod genomes. The decode types themselves apply to all breedable species.

Every gene in the genome has two jobs simultaneously: contributing to visual expression (what the specimen looks like) and contributing to stat expression (what the specimen's stats are). These two layers are independent — see The Dual-Layer Concept below.

For visual expression, different chromosomes (or regions within a chromosome) read their genes in different ways to produce different kinds of output. The way a chromosome reads its genes is called its decode type.

There are three known decode types in Project Gorgon's genetics system.

Decode Type 1: Switch

How it works: Binary on/off. A specific pattern of alleles either activates a trait or does not. There is no spectrum or range — the trait is either present or absent.

Examples:

• Glow: Certain allele combinations activate glow. Others do not.
• Particles: Certain patterns activate particles at specific body positions. Other patterns produce no particles.
• Leg deformities: Each leg can independently be normal or deformed, with each leg controlled by its own switch.

Key characteristics:

• Output is discrete: ON or OFF. No middle ground.
• Multiple allele patterns can produce the same outcome (many different patterns can all result in "glow ON").
• The specific pattern determines sub-variations within the ON state (for example, in arthropod genomes, tail particles vs wing particles are different ON states, not just "particles ON").

Decode Type 2: Series

How it works: Pattern-matched output. The specific combination of alleles across the region maps to a specific output from a defined set of possibilities. Think of it as a lookup table — this exact pattern produces this exact result.

Example: Tail light color. The allele pattern across a specific gene region determines which color the tail light displays. Each unique pattern maps to one specific color from the known set (Wave Teal, Poison Green, Golden Yellow, Aqua Blue, Red Orange, Firey Pink, Normal Purple, Galaxy Purple, Sparkle Purple, White/Purp/Teal, White Frosty, White Noise, or no tail light at all).

Key characteristics:

• Output is discrete but with many possible values (not just on/off).
• The entire pattern matters — changing one allele can change the output entirely.
• There is no gradient or spectrum between outputs. A specimen's tail light is one specific color, not "between" two colors.

Reading rule for series: When reading the allele pattern for visual output, treat mixed (⦿) as dominant (⬤). Mixed behaves like dominant for determining which output is displayed. However, for BREEDING purposes, mixed is still mixed and needs clarifying.

Decode Type 3: Graduation

How it works: Spectrum/scale. The ratio of dominant (⬤) to recessive (〇) alleles across the region determines where a trait falls on a continuous range. More dominant pushes the trait one direction; more recessive pushes it the other direction.

Examples:

• Body color hue: The balance of dominant vs recessive across an entire chromosome determines the body's hue on a color spectrum.
• Body color saturation: The dominant/recessive ratio determines saturation intensity.
• Body scale: The ratio determines the size of a body part on a scale.

Key characteristics:

• Output is continuous, not discrete. The trait slides along a range.
• Individual allele positions may not matter as much as the overall ratio of dominant to recessive across the region.
• Changing one allele slightly shifts the trait along the spectrum rather than flipping it to a completely different output.

Two Sub-Types of Graduation

Circular: The spectrum wraps around so that all-dominant and all-recessive produce the same (or similar) output. Like a color wheel where 0 degrees and 360 degrees are both red. Circular graduation is used for hue, because hue is inherently circular in color theory.

Linear: The spectrum has two distinct endpoints. All-dominant produces one extreme, all-recessive produces the other. Used for saturation, brightness, and body/part scale.

Open research question: In a graduation, do all gene positions contribute equally to the ratio, or do some positions weigh more heavily than others? This is unconfirmed and flagged for future research. If unequal weighting exists, changing certain positions would shift the trait more than changing others.

Decode Type Summary

Decode Type	How It Reads	Output Type	Example
Switch	Specific pattern	Binary (on/off)	Glow, particles
Series	Pattern lookup table	Discrete set	Tail light color
Graduation	Dominant/recessive ratio	Continuous range	Body color, scale

Circular and Linear are sub-types of Graduation, not separate decode types.

The Dual-Layer Concept

Every gene position in the genome contributes to two independent layers simultaneously:

1. Visual expression — what the specimen looks like (color, glow, scale, particles, body deformity)
2. Stat expression — what the specimen's stats are (Ferocity, Toughness, etc. for arthropods; Temperament, Toughness, etc. for horses)

These two layers operate independently. A gene on a color chromosome still sometimes has a stat value. A stat gene still has a visual expression value. The same physical gene position affects both layers at once, but the two effects do not interfere with each other — changing a gene's state affects both its visual output and its stat contribution simultaneously.

Why This Matters for Breeding

Clarifying a line for visual traits involves the same genes that contribute to stats. When a breeder optimizes for a specific color or visual appearance, they are locking genes at specific states (⬤ or 〇) to achieve that visual output. But those same locked states also determine the stat contribution of those genes.

This means that optimizing for a specific visual expression can sometimes require accepting a slightly lower stat value at certain positions — and vice versa. A breeder who wants a specific body color may need to hold some genes at ⬤ (dominant) for the visual, even though 〇 (recessive) would give a stat bonus for arthropods.

This is a genuine tradeoff that every serious breeder eventually faces:

• Pure stat optimization: breed all stat genes to 〇, accept whatever visual expression results
• Pure visual optimization: breed genes to the state the visual requires, accept whatever stat expression results
• Balanced approach: optimize stats where the visual decode allows it, and accept visual compromises where stat optimization is the priority

There is no single correct answer. The right tradeoff depends on what the breeder is trying to achieve. Understanding the dual-layer concept is what allows a breeder to make that decision intentionally rather than by accident.

Species Differences

For arthropods, stats express only at double recessive (〇). This makes the tradeoff relatively straightforward — any gene held at ⬤ (dominant) or ⦿ (mixed) for visual purposes is a gene that does not contribute to stats.

For horses, the dual-layer concept is more complex because some stat genes express at ⬤ rather than 〇, and some genes are dual-stat (expressing one stat at ⬤ and a different stat at 〇). See the Horse Genome Structure article for the full detail.

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Research and knowledge by Kaskrim. Compiled by AI Elara. Project Gorgon Genetics Research.

This article is part of the Project Gorgon Genetics Research series by Kaskrim.