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Evolutionary Biology
Genomics and evolution
| Question | Answer |
|---|---|
| What is genomics? | The study of the “entire hereditary information” in an organism, which is mostly encoded in the genome |
| Assembling a genome with ‘shotgun’ sequencing | • Collect the organism and extract a lot of high-quality DNA • break into fragments • read the fragments with a high-throughput sequencer • piece together the fragments • interpret the sequence (annotation) |
| De novo genome assembly | Is like piecing together an encyclopaedia from 300-500-letter fragments of sentences |
| Sequencing technology – ever evolving | Long-read sequencing = less rebuilding needed afterwards! Better for reading repetitive regions of the genome … … contains more error |
| Analysis of DNA Sequence Information | Locate regulatory sequences (known from years of painstaking experimental work) and open reading frames (ORFs = stretches of DNA sequence without stop codons) |
| Analysis of DNA Sequence Information | Annotation of genes (assignment of gene to functional groups) |
| What good are genomes? | • To reconstruct better phylogenies (phylogenomics) • Cancer genomics • Identification of regions likely involved in disease • To identify species that are suffering from low genetic diversity |
| Genomes are themselves interesting to study | Size, number of genes, gene families |
| Genome sizes and gene number can be (partially) explained by life history | Buchnera bacteria live in the gut of the pea aphid, produce nutrients for the aphid, and receive nutrients from the aphid |
| Buchnera’s genome is 0.64 Mbp (640,000 bp), which is 1/8 the size of E. coli (~5 Mbp) | Compared to E. coli, many genes are missing from Buchnera’s genome for synthesis of amino acids etc |
| Buchnera’s genome is 0.64 Mbp (640,000 bp), which is 1/8 the size of E. coli (~5 Mbp) | Buchnera’s genome does have the genes necessary for synthesising the amino acids that the aphid host cannot make (the ‘essential’ amino acids for the host) |
| Comparative genomics | The traditional approach to uncovering the genetic basis of interesting phenotypes - The ‘candidate gene’ approach |
| Comparative genomics | 1. What if you have no ‘candidate genes’? 2. How do you know that your candidates are the most important and not just the ones that you happened to test? 3. Every phenotype is really governed by many genes at once, and you want to find all of them |
| What genes are involved in echolocation? | ie. microbats, toothed whales - the prestin gene: associated with other adaptive changes through the genome - Alternative (false) phylogeny that groups all the echolocating species together - 400-800 genes that supported the echolocators-together tree |
| We can compare individuals within a single species, using “resequencing” | Once you have a high-quality, reference genome, the genomes of subsequent individuals from the same species are much easier to assemble With genome resequencing, it is possible to compare cancerous and healthy cells from the same patient |
| Genomes let us find useful natural products, like new antibiotics | ➢ >60% of our antibiotics come from the actinomycete bacteria, which are grown in Petri dishes and challenged with pathogenic bacteria and fungi ➢ But bacteria only release a very few of their antibiotic compounds in culture |
| Evolutionary conserved regions are the interesting regions | Mutations in these positions in any given individual are more likely to be fitness-reducing mutations (= deleterious mutations) |
Created by:
rose.coo
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