2022-2023 Laura van den End
1. Introduction
What de nes a model organism Homology and synteny
- Model organism: species is extensively studied to - Homology: emerged in two organisms by shared
understand particular biological phenomena, with ancestry ~ genes or structures can be homologous
the expectation that the model will provide insight - Paralogs: 2 homologous genes that are a
into the workings of other organisms or general product of gene duplication (same organism)
biological processes. ~ variety of topics by many - Orthologs: 2 homologous genes that are a
groups Model system: used to study very product of speciation (different organisms)
specific topic by few groups - Genomics: study of molecular organization of
- E.g to explore potential causes and treatments for genomes, their information content and the gene
human diseases products they encode ~ 3 main areas
- Made possible by the common descent of all living 1. Structural: physical nature of genomes
organisms, and the conservation of metabolic and 2. Functional: how genome functions
developmental pathways and genetic material 3. Comparative: compare entire genomes
over the course of evolution between organisms
- Evolution: feedback loop of changes in genes - The genome of most model organisms were
which lead to different phenotypes → determined using whole genome sequencing
different changes in fitness ~ environmental like Sanger Sequencing
pressure needed - Synteny: finding genes in comparable places ~
- Mendel’s peas: model system or organism? You conserved positions throughout evolution
look at something in peas that is true in other
plants and for a part in humans. However it is not Comparative genomics
widely studied → system - Understand evolution, improve crops, identify
genetic base of disease
Selecting a model organism - Genetic information is exchangeable
- When not looking at ethics: take the one closest, - Many genes are conserved over organisms →
but it mainly depends on the question A gene from one organism can often still
function in an organism of a very diff species
Dynamics of evolutionary innovation - Not necessarily the same function
1. Potentiation: there is no mutation yet, but it - Genome size is unrelated to complexity
forms a potentiation to, with other mutations, - E.g. Fugu genome is much smaller than
obtain the advantage human, but comparable number of genes
2. Actualisation - C-value = weight of genome (looking at
3. Refinement haploid, bc diploid just has the copy of the
info, not more info.
- Gene expression is a crucial difference between
Types of model systems
- Genetic: amendable to genetic analysis, i.e. breed organisms ~ e.g. speech
- Single mutation in FOXP2 gene damages
large numbers + short generation time → large
speech but not language comprehension
scale crosses → follow over several generations
- Many mutations available and detailed - FOXP2 has 2 or 3 aa different in primates and
mice → we have speech and they don’t
genetic map can be created
- Experimental: not necessarily genetic amendable
- Other exp advantages, often in development Genome evolution
- Genomic: regardless of genetic or experimental - Polyploidy ~ more copies → bigger organisms
(dis)advantages, species are chosen because of the - Autopolyploidy: genome is duplicated (1 sp)
quality of their genome or they occupy a pivotal - Allopolyploidy: hybridization + duplication
position in the evolutionary tree of genomes of 2 different species
- Is mycoplasma spp a model organism? It has - Horizontal gene transfer: genes hitchhike from
the smallest genome, so it is easily studied. other species; sometimes organisms swap genes/
But it is only used for one question, so no can result in homologous genes in very diff org.
Modelorganisms in biological research
↔︎fi
, 2022-2023 Laura van den End
2. Browsing through model
organisms
Prokaryotes Fungi
- Life on earth is ≥ 3.4 billion years old → started A. nidulans Metabolism and DNA repair, has 3 life
with prokaryotes cycles (sexual, asexual, parasexual)
- Some important prokaryotes:
N. crassa Meiosis, metabolic regulation and
E. coli cicardian rhythms
B. subtilis Sporulation, resistance and biofilms U. maydis Plant disease, recombination, DNA repair
and cell migration
C. crescentus Cell differentiation and “decision” making
Yeast See chapter 3
M. genitalium Small genome and synthetic life
A. Fisheri Bioluminescence, animal-bacterial
symbiosis Beadle-tatum experiment
N. crassa → does our genetic information hold the
Synechocystis Photosynthesis code to make enzymes?
P. fluorescens Comparison of diversified lab strains - One gene - one enzyme hypothesis: each gene
codes for an individual enzyme and thus impacts
a specific step in a metabolic pathway
Protista 1. Damage DNA with X-Rays → create mutants
- All eukaryotes not belonging to Plantae, Animalia, 2. Cross mutants with wild type
Fungi 3. Grow the offspring on complete (with aa) and
C. reinhardti Photosynthesis, flagella and motility, regu- minimal media (without aa)
lation of metabolism, cell-cell recognition 4. Look for mutant that grows on complete, but not
and adhesion, response to nutrient on minimal media → find a mutant that not
deprivation produces a certain aa
D. discoideum Cell communication, differentiation and 5. Grow on media with a single aa to identify in
programmed cell death which aa (pathway) the mutation occurred
- We now know that genes also codes for proteins
Sporulation, resistance and biofilms
T. thermophila Fundamental functional genomics Invertebrates
- C.elegans and D. melanogaster are excellent genetic
Choanoflagellate Closest single cell relatives of animals
models (see chapter 4 and 5
Hydra Evolution of animal and bilaterian body
Plants plans
A. thaliana See chapter 6 E. scolopes Animal-bacteria symbiosis, bioluminescent
Z. mays Facilitated discovery of transposons P. Pacificus Evolutionary developmental biology and
(roundworm) comparative analysis with C. elegans
O. sativa (rice) One of the smallest genomes of any cereal
species S. roscoffensis Bilaterian body plan development
(flatworm)
M. truncatula Model legume, symbiosis responsible for
nitrogen fixation T. castaneum Behavioral ecology and development
(flour beetle)
N. tabacum Tabacco BY-2 cell line, general plant
physiology studies on cellular level Sea urchin Embryological studies
P. patens Non-vascular (“primitive”) plant with its Aplysia Response model in neurobiology and
genome completely sequenced, evolution (sea slug) model of cytoskeletal rearrangements
Populus Model in forest genetics and woody plant - Chordates: B. lanceolatum (development) and C.
studies intestinalis (NS development and metamorphosis)
Modelorganisms in biological research
, 2022-2023 Laura van den End
Vertebrates
Fish
D. rerio (zebrafish) See chapter 7
O. latipes (medaka) Zebrafish of the east
N. furzeri (killifish) Aging and development
T. rubripes
(puffer fish)
Amphibians
X. laevis Large embryos, high tolerance for
(African clawed frog) physical and pharmacological manipu-
lation
X. tropicalis
Birds
G. gallus domesticus Developmental studies, excellent dor
(chicken) micro-manipulation and overexpres-
sion of gene products
T. guttata Song system of songbirds and non-
(zebra finch) mammalian auditory systems
Rodents
M. musculus (mouse) Inbred lines, selected for particular
traits, often of medical interest
R. norvegicus (rat) More prone to learn, toxicology,
neuro-logy, source of primary cell
structures
H. glaber Ageing and cancer research, live 30
(naked mole-rat) years and highly resistant to cancer
C. porcellus Formerly used as host for bacterial
(Guinea pig) infections
S. hispidus Formerly used in polio research
(cotton rat)
C. auratus First used to study Kala-azar (leish-
(golden hamster) maniasis)
Other mammals
C. lupus familiaris Respiratory and cardiovascular model
(dog)
M. mulatta Infectious disease and cognition
(rhesus monkey)
Modelorganisms in biological research
1. Introduction
What de nes a model organism Homology and synteny
- Model organism: species is extensively studied to - Homology: emerged in two organisms by shared
understand particular biological phenomena, with ancestry ~ genes or structures can be homologous
the expectation that the model will provide insight - Paralogs: 2 homologous genes that are a
into the workings of other organisms or general product of gene duplication (same organism)
biological processes. ~ variety of topics by many - Orthologs: 2 homologous genes that are a
groups Model system: used to study very product of speciation (different organisms)
specific topic by few groups - Genomics: study of molecular organization of
- E.g to explore potential causes and treatments for genomes, their information content and the gene
human diseases products they encode ~ 3 main areas
- Made possible by the common descent of all living 1. Structural: physical nature of genomes
organisms, and the conservation of metabolic and 2. Functional: how genome functions
developmental pathways and genetic material 3. Comparative: compare entire genomes
over the course of evolution between organisms
- Evolution: feedback loop of changes in genes - The genome of most model organisms were
which lead to different phenotypes → determined using whole genome sequencing
different changes in fitness ~ environmental like Sanger Sequencing
pressure needed - Synteny: finding genes in comparable places ~
- Mendel’s peas: model system or organism? You conserved positions throughout evolution
look at something in peas that is true in other
plants and for a part in humans. However it is not Comparative genomics
widely studied → system - Understand evolution, improve crops, identify
genetic base of disease
Selecting a model organism - Genetic information is exchangeable
- When not looking at ethics: take the one closest, - Many genes are conserved over organisms →
but it mainly depends on the question A gene from one organism can often still
function in an organism of a very diff species
Dynamics of evolutionary innovation - Not necessarily the same function
1. Potentiation: there is no mutation yet, but it - Genome size is unrelated to complexity
forms a potentiation to, with other mutations, - E.g. Fugu genome is much smaller than
obtain the advantage human, but comparable number of genes
2. Actualisation - C-value = weight of genome (looking at
3. Refinement haploid, bc diploid just has the copy of the
info, not more info.
- Gene expression is a crucial difference between
Types of model systems
- Genetic: amendable to genetic analysis, i.e. breed organisms ~ e.g. speech
- Single mutation in FOXP2 gene damages
large numbers + short generation time → large
speech but not language comprehension
scale crosses → follow over several generations
- Many mutations available and detailed - FOXP2 has 2 or 3 aa different in primates and
mice → we have speech and they don’t
genetic map can be created
- Experimental: not necessarily genetic amendable
- Other exp advantages, often in development Genome evolution
- Genomic: regardless of genetic or experimental - Polyploidy ~ more copies → bigger organisms
(dis)advantages, species are chosen because of the - Autopolyploidy: genome is duplicated (1 sp)
quality of their genome or they occupy a pivotal - Allopolyploidy: hybridization + duplication
position in the evolutionary tree of genomes of 2 different species
- Is mycoplasma spp a model organism? It has - Horizontal gene transfer: genes hitchhike from
the smallest genome, so it is easily studied. other species; sometimes organisms swap genes/
But it is only used for one question, so no can result in homologous genes in very diff org.
Modelorganisms in biological research
↔︎fi
, 2022-2023 Laura van den End
2. Browsing through model
organisms
Prokaryotes Fungi
- Life on earth is ≥ 3.4 billion years old → started A. nidulans Metabolism and DNA repair, has 3 life
with prokaryotes cycles (sexual, asexual, parasexual)
- Some important prokaryotes:
N. crassa Meiosis, metabolic regulation and
E. coli cicardian rhythms
B. subtilis Sporulation, resistance and biofilms U. maydis Plant disease, recombination, DNA repair
and cell migration
C. crescentus Cell differentiation and “decision” making
Yeast See chapter 3
M. genitalium Small genome and synthetic life
A. Fisheri Bioluminescence, animal-bacterial
symbiosis Beadle-tatum experiment
N. crassa → does our genetic information hold the
Synechocystis Photosynthesis code to make enzymes?
P. fluorescens Comparison of diversified lab strains - One gene - one enzyme hypothesis: each gene
codes for an individual enzyme and thus impacts
a specific step in a metabolic pathway
Protista 1. Damage DNA with X-Rays → create mutants
- All eukaryotes not belonging to Plantae, Animalia, 2. Cross mutants with wild type
Fungi 3. Grow the offspring on complete (with aa) and
C. reinhardti Photosynthesis, flagella and motility, regu- minimal media (without aa)
lation of metabolism, cell-cell recognition 4. Look for mutant that grows on complete, but not
and adhesion, response to nutrient on minimal media → find a mutant that not
deprivation produces a certain aa
D. discoideum Cell communication, differentiation and 5. Grow on media with a single aa to identify in
programmed cell death which aa (pathway) the mutation occurred
- We now know that genes also codes for proteins
Sporulation, resistance and biofilms
T. thermophila Fundamental functional genomics Invertebrates
- C.elegans and D. melanogaster are excellent genetic
Choanoflagellate Closest single cell relatives of animals
models (see chapter 4 and 5
Hydra Evolution of animal and bilaterian body
Plants plans
A. thaliana See chapter 6 E. scolopes Animal-bacteria symbiosis, bioluminescent
Z. mays Facilitated discovery of transposons P. Pacificus Evolutionary developmental biology and
(roundworm) comparative analysis with C. elegans
O. sativa (rice) One of the smallest genomes of any cereal
species S. roscoffensis Bilaterian body plan development
(flatworm)
M. truncatula Model legume, symbiosis responsible for
nitrogen fixation T. castaneum Behavioral ecology and development
(flour beetle)
N. tabacum Tabacco BY-2 cell line, general plant
physiology studies on cellular level Sea urchin Embryological studies
P. patens Non-vascular (“primitive”) plant with its Aplysia Response model in neurobiology and
genome completely sequenced, evolution (sea slug) model of cytoskeletal rearrangements
Populus Model in forest genetics and woody plant - Chordates: B. lanceolatum (development) and C.
studies intestinalis (NS development and metamorphosis)
Modelorganisms in biological research
, 2022-2023 Laura van den End
Vertebrates
Fish
D. rerio (zebrafish) See chapter 7
O. latipes (medaka) Zebrafish of the east
N. furzeri (killifish) Aging and development
T. rubripes
(puffer fish)
Amphibians
X. laevis Large embryos, high tolerance for
(African clawed frog) physical and pharmacological manipu-
lation
X. tropicalis
Birds
G. gallus domesticus Developmental studies, excellent dor
(chicken) micro-manipulation and overexpres-
sion of gene products
T. guttata Song system of songbirds and non-
(zebra finch) mammalian auditory systems
Rodents
M. musculus (mouse) Inbred lines, selected for particular
traits, often of medical interest
R. norvegicus (rat) More prone to learn, toxicology,
neuro-logy, source of primary cell
structures
H. glaber Ageing and cancer research, live 30
(naked mole-rat) years and highly resistant to cancer
C. porcellus Formerly used as host for bacterial
(Guinea pig) infections
S. hispidus Formerly used in polio research
(cotton rat)
C. auratus First used to study Kala-azar (leish-
(golden hamster) maniasis)
Other mammals
C. lupus familiaris Respiratory and cardiovascular model
(dog)
M. mulatta Infectious disease and cognition
(rhesus monkey)
Modelorganisms in biological research
