Genomes, Genomics, and GMOs

Genome sequencing has transformed biology by

allowing scientists to examine the entire genetic blueprint of an organism, rather than individual genes in isolation

The first genome ever sequenced

bacteriophage, an organism with an RNA genome that codes for only four protein( very simple)

the first eukaryotic genome

sequenced in 1996 and belonged to yeast (Saccharomyces cerevisiae).

eukaryotic genomes

are larger, contain repetitive DNA, and require more complex annotation

Caenorhabditis elegans

the first multicellular animal with a fully sequenced genome.

Repetitive DNA is a major sequencing challenge

consists of sequences that occur multiple times throughout the genome. These regions are notoriously difficult to sequence and assemble, because short reads cannot easily be assigned to their correct genomic location.

When sequencing a new organism, researchers face a fundamental trade-off between

depth versus breadth

Depth

refers to sequencing the same genome repeatedly to achieve high accuracy

Breadth

• refers to sequencing many individuals or species with lower coverage.

Because sequencing generates massive amounts of data

data analysis and storage often cost more than the actual sequencing itself

The three major analytical stages in sequence generation

Primary Analysis

Secondary Analysis

Tertiary Analysis

Primary Analysis

Raw sequence data generated directly by the sequencing machine

Secondary Analysis

Quality control and filtering of reads to remove errors and artifacts

Tertiary Analysis

Integrating multiple datasets to make biological meaning, such as identifying genes under selection or comparing populations.

Genomics has historically been biased toward

model organisms, particularly vertebrates and mammals, because of their relevance to human biology

Why sequencing non-model organisms are important

genomic data from these organisms often reflect phylogenetic history, allowing scientists to reconstruct evolutionary relationships even in poorly studied taxa.

Comparative genomics

examines differences and similarities across genomes to understand function and evolution

When studying Comparative genomics researchers compare

• Gene content

• Gene order

• Regulatory sequences

• Non-coding DNA

• Structural landmarks

Orthologous genes

diverged after a speciation event and often retain similar functions across species.

Paralogous genes

• diverged after a gene duplication event, allowing new or specialized functions to evolve.

Comparing non-model organisms to model organisms provides

a starting point for testing speciation hypotheses, reconstructing evolutionary history, and guiding conservation decisions.

Types of Genomics

• Evolutionary genomics (e.g. when vertebrates colonized land)

• Population genomics

• Landscape genomics / phylogenomics

• Speciation genomics

• Conservation genomics

Most of these fields would not exist without next-generation sequencing (NGS).

Transcriptomics

RNAs are being expressed

Proteomics

proteins produced and their structures

Metabolomics

• hormones and signaling molecules

Epigenetics

heritable changes in gene expression without DNA sequence changes

What Are GMOs?

A Genetically Modified Organism (GMO) contains one or more genes from another organism, inserted using molecular biology techniques

Concerns About GMOs

• Genetic pollution

• Out-competition of wild types

• Gene flow to new hosts

• Effects on non-target species

Horizontal gene transfer mechanisms include

• Conjugation (F plasmids)

• Transformation (free DNA)

• Transduction (virus-mediated)

CRISPR/Cas9 originates from

bacterial immune system used to silence viral DNA.

CRISPR/Cas9 allows

scientists to precisely cut and insert DNA sequences into almost any genome.

CRISPR enables

gene insertion and regulation, making it far more precise than earlier GMO techniques.