Genome

**Genome** is the genetic structure of codons, storing data and instructions how to replicate it using DNA. It's present in all lifeforms, encoding organism characteristics in compressed form. Genomes are uniform across species, with differences between specimens expressed and coded by genotypes. It's genetic layout can be sequenced, allowing codon mapping for genotype altering purposes. Genome is present in every cell of all living organisms, and is inherited down in process of reproduction.

## Structure

Genome consists of DNA, represented by AT-GC base pairs. Each of three base pairs are called codons, and encode single amino-acid. A set of amino-acids builds the genome. Genomes start and end with special codons, called translation markers, and contain DNA in unique order between. Each codon in every genome can be either vital or coding. Most codons in genome are always vital. There is no obvious, visual difference between coding and vital codons, and their type has to be determined by trial and error or deduction with genotype marker mapping.

### Vital codons

Vital codons encode for critical cell reproduction processes, and any change in them will always result in cell replication failure, leading directly to organism death.

### Coding codons

Coding parts of genome contain genotype, expressed as organism characteristics and behaviours, and can vary within range of compatible amino acids. Plants have 25 coding codons in genome, while animals have 31.

### Translation markers

Translation marker codons are neither vital nor coding, but editing them will have same result as editing vital codons. "Translation start" is always encoded with ATG codon, and most often ends with TGC "translation stop" codon.

### Codon synonymity

Some amino-acids can be encoded using multiple, different DNA combinations. In most cases, only amino-acid type matters in genome for gene expression, making the codon synonymous. Synonymous codon DNA expression will always have the same result across all possible amino-acid AT-GC combinations. Non-synonymous codons contain information not only in codon amino-acid type, but also in the specific DNA combination used to build the amino-acid. Using different AT-GC combinations of same amino-acid will cause observable differences in genotype expression for non-synonymous codons. Codon synonymity can be determined by genotype mapping, as certain characteristics will have always corresponding synonymous/non-synonymous codon.

## Mutations

Genomes represent fragile and complex structure, that can be altered and damaged by radiation/chemical reactions, or in the process of sexual reproduction, where parent genotypes are used to encode offspring genome. Random mutations are caused mostly by ionizing radiation, particles of very high speed and big enough mass to damage DNA while passing through cells, but can be also invoked directly with chemicals like acids and solvents, physically damaging genome chain, or viruses and bacteria interference.

### Mutagens

Artificially invoked chemical mutations are caused by carcinogens and mutagens. Carcinogens are mutagens known to cause vital codons mutation, and can lead to cell reproduction failure. "Plain" mutagens alter only coding parts of genome.

### Cross-polination

Flowering plants can mutate by exchanging pollen. Pollen can be artificially used in cross-pollination between two flowering plant species. Pollinated plant will always inherit some characteristics from genotype of pollinating specimen.

### Natural mutation inheritance

Animal genome is always inherited from parent, including all mutations present at the moment of heir conception. This is not true in plants - for gameplay reasons, genotype inherited by seed is always passed from plant root, stopping natural, random mutations from propagating across plants, and allowing control and selection over growing flora species.

### Artificial mutation inheritance

Animal genotype inheritance can be forced by creating new animal family from specimen with interesting characteristics. Selected animal will pass all of its mutations to the offspring. Plant mutations can be artificially passed down by taking cuttings of mutated plant parts, and planting them. Resulting plant root (and all of heir plant roots) will contain the DNA of original cutting.

### Structural mutations

Some mutations are so severe that genome order changes for all codons. Structural mutations in animals are caused by exceeding threshold of enviroment adaptation changes, resulting in new animal order emerging. In plants, structural mutations happen when codons describing plant branching are altered. Trees, bushes, flowers and grasses can share same genome, as long as plant branching structure doesn't drastically change. For example, while plant height mutation is not structural, mutation causing plant to start flowering - is.

## Genome research

Genomes can be researched, allowing genotype reading, altering and storing for future research. Performing any genome research requires active research specimen, with undamaged DNA. Any genome research is always unique and relevant only to vivarium tank that the research has been originally done in.

### Sequencing

To read and alter genome, it has first to be sequenced. Basic genome sequencing process takes time to finish, but with enough research progress and experience the process can be done instantly. Once genome is sequenced, its structure will be known and readable for all organisms of same chromosome count. However, if structural mutation happens - the resulting, new genome will be no longer compatible/readable, and will require new sequencing process.

### Storing

After sequencing, genotype can be saved into one of 5 DNA storage slots. Once the genome is stored, it can be displayed in stored genome window, and be directly compared with active specimen genome, allowing the process of genome mapping, by searching for differences between genotypes and marking found codons with descriptions.

### Superseding

All sequenced genomes can be altered, by changing DNA base pairs in genome codons. Superseding vital codons, or applying incompatible amino-acid to coding parts of genome will cause genotype errors, and kill the superseded specimen. Gene editing tools get better with research and experience. Basic x-ray radiating tool has high chance for random, unintended mutations to occur, resulting in very high mortality chance. Advanced genome editing methods use more sophisticated solutions, like CRISPR-Cas9 bacteriophage, to avoid random or rule out unintended, often harmful mutations.