Genomics for Health and
Environment
NWI-BB086
12 EC
Year 3
Quarter 1
Biology – Bachelor
,L1 – Genomes
To see if the part of the genome came from the male or the female ancestor you should look at the
mitochondrial and chloroplastic DNA, as it will only be inherited from the female ancestor.
Prokaryotes pass genomes from one to each other. That’s why the evolutionary tree of prokaryotes
contain bridges (less branching off), keep meeting each other (genome passing).
Mitochondria and chloroplasts are endosymbiotic cells.
People’s DNA can be used to infer their geographic origin with surprising accuracy – often to within a
few hundred kilometres.
500,000 SNPs were analyzed in approximately 3,000 Europeans.
There are many types of ‘chromosomes’:
- Coliphage (sub-millimetre)
- E. coli (>1 millimetre)
- Higher eukaryotic chromosomes (around 108 bp)
As the prokaryotic chromosomes are so small and weigh so less it must therefore be condensed
around 1000 times to fit inside a bacterium.
The eukaryotic chromosomes are very long, a DNA condensation factor of around 1 million-fold is
therefore required to fit the human genome inside the nucleus.
A little bit more RNA than DNA is present in a bacterium. The amount depends on the species.
Eukaryotes also have 10-40 times more RNA than DNA.
The total amount of RNA in an average human cell ranges between 10 and 30 pg and it is estimated
to be distributed in 85% rRNA, 10-12% tRNA, and 2-5% mRNA.
Bacterial rRNAs and tRNAs make up 95-97% of the total RNA isolated from bacterial cells.
Nucleoid = in bacteria, co-transcriptional translation is the rule in bacteria.
In eukaryotes chromosomes are found in the nucleus.
Eukaryotes harbour 2 or 3 (or 4 or 5 or N) genomes.
Animals and Fungi:
- Chromosomes in the nucleus
- A circular chromosome in the mitochondria
Plants:
- Mitochondrial genomes
- Circular chromosomes in their chloroplasts
,Protists:
- A variety of ‘unicellular’ organisms harbour extra endosymbionts that have their own
chromosome(s).
All these organisms may harbour phage/viral genomes
Multicellular organisms are populated by a plethora of bacteria, fungi and protists – e.g.; a human
gut harbours as many or even more non-human cells as a human body has diploid cells.
When you sequence DNA, expect other DNA to be there.
Mitochondrial size from small to large:
Animal → Fungi → Plants
Chloroplast chromosomes are circular and are related to prokaryotic chromosomes.
Usually they are 120000 – 160000 bp.
Hence they code for more proteins than animal mitochondria.
Pseudogenes: does not have an impact over the genome. It lacks an open reading frame and does
not contain a stop codon, it is a fake gene. Eukaryotes contain the same amount of pseudogenes as
normal genes.
To see if species are related to each other, look at the amount of shared transposons (at a specific
position).
Mechanisms of chromosome evolution:
(Mutagenesis/clastogenesis):
- Gene duplication, usually via homologous recombination (e.g., during collapsed DNA
replication fork rescue)
- Pseudogene formation
- Whole genome duplications
- Endosymbiosis
- Transposons (SINE, LINE, Retroelements)
- Mutations (point mutation, deletion, insertions, inversions, duplications)
- Cross over/recombination
- Exon shuffling (the likely accelerator of eukaryotic evolution over the last 500 million years)
- Genome reduction and gene loss (“less is more”)
- Frame shift → nonsense → pseudogene
- Horizontal gene transfer
- Sexual reproduction, meiosis → cell fusion
1.5% of the DNA codes for proteins.
, L2 – Introduction Metagenomics
Microbial perspective: species diversity and metabolic potential in microbial communities
- To understand biodiversity and activities of microorganisms in nature and to monitor their
effects on ecosystems.
- The majority of microbial biodiversity cannot be captured by cultivation based methods →
can (meta)genomics help?
Crystal ball prediction = discovered by Carl Woese, genome sequencing has come of age, and
genomics will become central to microbiologys future.
Metagenomics: environmental and community genomics is the genomic analysis of microorganisms
by direct extraction and cloning of DNA from an assemblage of microorganisms (ecosystem).
Problems to be solved by metagenomics:
- Which species are present and what is their abundance?
- Which functions are present/absent?
- Who is active?
Phylomarker (has to be present anywhere in all organisms, 16S and 23S ribosomes rRNA) and
functional markers (a marker specific for anammox bacteria for example) should be used.
Metagenomics:
- Classical genomics and microbiology largely rely on isolating individual microbial species in
pure cultures.
- Thus far, only a miniscule fraction (1%) of the estimated millions of microbial species on
Earth can be cultured.
- Metagenomics allows to access a community’s genome without relying on pure cultures.
- Metagenomics transcends the limitations of classical genomics and microbiology.
- Metagenomics gives scientists access to millions of microbes that have not previously been
studied & is very helpful designing novel cultivation strategies.
Metagenomics questions:
- Within an environment:
o What biological functions are present (absent)?
o What organisms are present (absent)?
- Compare data from (dis)similar environments
o What are the fundamental rules of microbial ecology?
- Adapting to environmental conditions?
o How?
o Evidence and mechanisms for lateral transfer
- Search for novel proteins and protein families
o And diversity within known families
Importance of metagenomics:
- Soil health: A community of microorganisms are required to recycle nutrients. Farmers want
to know what is there (what a good soil is).
Environment
NWI-BB086
12 EC
Year 3
Quarter 1
Biology – Bachelor
,L1 – Genomes
To see if the part of the genome came from the male or the female ancestor you should look at the
mitochondrial and chloroplastic DNA, as it will only be inherited from the female ancestor.
Prokaryotes pass genomes from one to each other. That’s why the evolutionary tree of prokaryotes
contain bridges (less branching off), keep meeting each other (genome passing).
Mitochondria and chloroplasts are endosymbiotic cells.
People’s DNA can be used to infer their geographic origin with surprising accuracy – often to within a
few hundred kilometres.
500,000 SNPs were analyzed in approximately 3,000 Europeans.
There are many types of ‘chromosomes’:
- Coliphage (sub-millimetre)
- E. coli (>1 millimetre)
- Higher eukaryotic chromosomes (around 108 bp)
As the prokaryotic chromosomes are so small and weigh so less it must therefore be condensed
around 1000 times to fit inside a bacterium.
The eukaryotic chromosomes are very long, a DNA condensation factor of around 1 million-fold is
therefore required to fit the human genome inside the nucleus.
A little bit more RNA than DNA is present in a bacterium. The amount depends on the species.
Eukaryotes also have 10-40 times more RNA than DNA.
The total amount of RNA in an average human cell ranges between 10 and 30 pg and it is estimated
to be distributed in 85% rRNA, 10-12% tRNA, and 2-5% mRNA.
Bacterial rRNAs and tRNAs make up 95-97% of the total RNA isolated from bacterial cells.
Nucleoid = in bacteria, co-transcriptional translation is the rule in bacteria.
In eukaryotes chromosomes are found in the nucleus.
Eukaryotes harbour 2 or 3 (or 4 or 5 or N) genomes.
Animals and Fungi:
- Chromosomes in the nucleus
- A circular chromosome in the mitochondria
Plants:
- Mitochondrial genomes
- Circular chromosomes in their chloroplasts
,Protists:
- A variety of ‘unicellular’ organisms harbour extra endosymbionts that have their own
chromosome(s).
All these organisms may harbour phage/viral genomes
Multicellular organisms are populated by a plethora of bacteria, fungi and protists – e.g.; a human
gut harbours as many or even more non-human cells as a human body has diploid cells.
When you sequence DNA, expect other DNA to be there.
Mitochondrial size from small to large:
Animal → Fungi → Plants
Chloroplast chromosomes are circular and are related to prokaryotic chromosomes.
Usually they are 120000 – 160000 bp.
Hence they code for more proteins than animal mitochondria.
Pseudogenes: does not have an impact over the genome. It lacks an open reading frame and does
not contain a stop codon, it is a fake gene. Eukaryotes contain the same amount of pseudogenes as
normal genes.
To see if species are related to each other, look at the amount of shared transposons (at a specific
position).
Mechanisms of chromosome evolution:
(Mutagenesis/clastogenesis):
- Gene duplication, usually via homologous recombination (e.g., during collapsed DNA
replication fork rescue)
- Pseudogene formation
- Whole genome duplications
- Endosymbiosis
- Transposons (SINE, LINE, Retroelements)
- Mutations (point mutation, deletion, insertions, inversions, duplications)
- Cross over/recombination
- Exon shuffling (the likely accelerator of eukaryotic evolution over the last 500 million years)
- Genome reduction and gene loss (“less is more”)
- Frame shift → nonsense → pseudogene
- Horizontal gene transfer
- Sexual reproduction, meiosis → cell fusion
1.5% of the DNA codes for proteins.
, L2 – Introduction Metagenomics
Microbial perspective: species diversity and metabolic potential in microbial communities
- To understand biodiversity and activities of microorganisms in nature and to monitor their
effects on ecosystems.
- The majority of microbial biodiversity cannot be captured by cultivation based methods →
can (meta)genomics help?
Crystal ball prediction = discovered by Carl Woese, genome sequencing has come of age, and
genomics will become central to microbiologys future.
Metagenomics: environmental and community genomics is the genomic analysis of microorganisms
by direct extraction and cloning of DNA from an assemblage of microorganisms (ecosystem).
Problems to be solved by metagenomics:
- Which species are present and what is their abundance?
- Which functions are present/absent?
- Who is active?
Phylomarker (has to be present anywhere in all organisms, 16S and 23S ribosomes rRNA) and
functional markers (a marker specific for anammox bacteria for example) should be used.
Metagenomics:
- Classical genomics and microbiology largely rely on isolating individual microbial species in
pure cultures.
- Thus far, only a miniscule fraction (1%) of the estimated millions of microbial species on
Earth can be cultured.
- Metagenomics allows to access a community’s genome without relying on pure cultures.
- Metagenomics transcends the limitations of classical genomics and microbiology.
- Metagenomics gives scientists access to millions of microbes that have not previously been
studied & is very helpful designing novel cultivation strategies.
Metagenomics questions:
- Within an environment:
o What biological functions are present (absent)?
o What organisms are present (absent)?
- Compare data from (dis)similar environments
o What are the fundamental rules of microbial ecology?
- Adapting to environmental conditions?
o How?
o Evidence and mechanisms for lateral transfer
- Search for novel proteins and protein families
o And diversity within known families
Importance of metagenomics:
- Soil health: A community of microorganisms are required to recycle nutrients. Farmers want
to know what is there (what a good soil is).
