IB Biology HLClassifying Living DiversityPaper 1 & 2~12 min read
Uses of Genome Sequencing
Sequencing a genome used to take years and cost a fortune. Now it is fast, cheap and automated — and that has changed two things completely: how we work out which species are related to which, and how doctors choose a treatment for one particular patient.
📚 What you need to know
DNA sequencing identifies and records the base sequence of a genome. Methods are getting faster and cheaper, and most are now automated.
Newer methods are called next-generation sequencing (NGS).
Sequence data is analysed by computer for two main purposes: evolutionary relationships and personalised medicine.
Phylogenetics classifies species by their evolutionary origins and relationships, grouping them by shared common ancestry rather than appearance.
Three types of sequence data are used: DNA, mRNA and amino acid sequences.
The more similar the sequences, the more closely related the species, because species separated for longer accumulate more mutations.
Comparing multiple proteins or regions gives a more accurate estimate. A useful protein must be widespread and show sufficient variation — cytochrome c is a common choice.
Genomic medicine uses genome information to design treatments, screen for disease risk and predict response to drugs.
Sequencing has become routine
Sequencing determines the order of bases in an organism’s DNA. What has changed is not the idea but the speed. Modern next-generation sequencing is automated and rapid, so genomes that once took a whole international project are now produced routinely.
The data goes into computers running specialised programmes, which is where the biology actually happens. Two applications matter for this course.
Evolutionary relationships
Phylogenetics is the classification of species based on their evolutionary origins and relationships. Organisms are grouped by shared common ancestry, not by looking similar — which is exactly the weakness of the morphological approach.
Sequencing technology is especially useful in two awkward cases:
Comparing with an extinct species, using ancient DNA.
Separating species that are very physically similar and cannot be told apart by eye.
The logic behind the comparison
The principle is short and appears in almost every mark scheme:
The rule
The more similar the sequences, the more closely related the species
The reason is time. Two groups with very similar sequences separated into separate species more recently. Species separated for longer have had more time to accumulate mutations, and those mutations change the DNA, the mRNA transcribed from it, and the amino acid sequence of the resulting protein.
Read a tree from the branching points, not from how close two labels sit along the top. What matters is how far down the shared node is.
Choosing what to compare
Scientists pick specific proteins or regions of the genome to compare between organisms.
Looking at multiple proteins or multiple regions gives a more accurate estimate of how closely related organisms are than relying on one.
A useful protein must be present in a wide range of organisms, or there is nothing to compare, and must show sufficient variation between species, or every organism looks identical.
Cytochrome c is a common choice, because it is an integral protein in aerobic respiration and so occurs in a huge range of organisms.
Those two requirements pull in opposite directions, which is why the choice matters. A protein that varies wildly is useless if only a few species have it. A protein found everywhere is useless if it is identical everywhere. Cytochrome c sits in the sweet spot.
Personalised medicine
Information from projects like the Human Genome Project, which sequenced the entire human genome, is used to develop genomic medicine — using information about genes to design medical treatments. That information is stored in databases where genes coding for particular proteins can be found and analysed.
Application
How it works
The benefit
Targeted drugs
Knowing the sequence and structure of a protein involved in a disease allows drugs to be designed against it — for example an enzyme inhibitor if an enzyme is involved
Targeted treatments can mean fewer unpleasant side-effects
Genetic screening
Combining genome information with clinical and diagnostic data reveals patterns that indicate an individual’s risk of developing a disease
Preventative measures can be taken — for example, someone carrying a mutation known to raise breast cancer risk may choose surgery in advance
Lifestyle choices
Knowing a genetic risk of cancers or heart disease informs decisions about diet and lifestyle
Risk can be reduced before disease develops
Predicting drug response
A person’s genome indicates how well they might respond to a specific treatment
Treatment can be chosen on the basis of an individual’s genotype
🧠
Two uses, one dataset
Sequence data answers two very different questions: who is related to whom (phylogenetics) and what should this patient take (genomic medicine). Most exam questions are one or the other, so decide which before you start writing.
Worked examples
WE 1
Interpret sequence similarity
Species X shares 96% of a gene sequence with species Y, and 82% with species Z. Deduce the evolutionary relationships and explain your reasoning. (3 marks)
Step 1: the deduction
X is more closely related to Y than to Z.
Step 2: the reasoning
The more similar the sequences, the more recently the species separated from a common ancestor.
Step 3: why differences build up
Species separated for longer have had more time to accumulate mutations, so X and Z show a larger difference.
X and Y split more recently; Z branched off earlierexplain the mutation-over-time link — the deduction alone is only one mark
WE 2
Justify a choice of protein
Explain why cytochrome c is often chosen for comparing species. (3 marks)
Point 1: it is everywhere
Cytochrome c is an integral protein in aerobic respiration, so it is present in a wide range of organisms and can be compared across them.
Point 2: it varies enough
It shows sufficient variation between species for differences to be measured.
Point 3: improving accuracy
Comparing several proteins or regions rather than one gives a more accurate estimate of relatedness.
Widespread enough to compare, variable enough to be informativeboth requirements are needed — one on its own does not justify the choice
WE 3
Explain a benefit of genomic medicine
Explain how sequencing a patient’s genome can improve their treatment. (3 marks)
Point 1: risk
Combined with clinical data, the genome can indicate the patient’s risk of developing a disease, so preventative measures can be taken early.
Point 2: drug choice
It shows how well they are likely to respond to a specific treatment, so a drug can be selected on the basis of their genotype.
Point 3: targeted drugs
Knowing the structure of the proteins involved allows targeted drugs to be designed, which tend to cause fewer side-effects.
Earlier prevention, better-matched drugs, fewer side-effectsgive a concrete example, such as an enzyme inhibitor or screening for cancer risk
💡 Exam tips
Define phylogenetics as classification by evolutionary origins and relationships.
Say all three data types: DNA, mRNA and amino acid sequences.
Always explain similarity through time to accumulate mutations.
Give both requirements for a comparison protein: widespread and variable.
Name cytochrome c and say why it qualifies.
For medicine questions, give a specific application rather than “it helps doctors”.
⚠ Common mistakes
Reading a tree by how close the labels are. Relationships come from the branching points.
Saying more similar sequences mean more similar appearance. The claim is about relatedness.
Giving only one requirement for a protein used in comparison.
Confusing phylogenetics with morphological classification. One uses ancestry, the other appearance.
Saying genomic medicine cures genetic disease. It informs treatment and risk, which is not the same.
Forgetting mRNA when listing the types of sequence data.
Up next: Species Concept: Challenges — the organisms that reproduce without a partner, and the bacteria that swap genes sideways.
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