13. Genomics in use Flashcards
Explain what is comparative genomics
Comparative genomics - compare the complete genome sequences of different species - identify unique genes -> infer functional roles
What are the current pojects which will be useful in comparative genomics?
Earth biogenome project - aims to sequence all life on Earth - will be able to compare many species:
- UK initiative - Darwin Tree of Life
- EU initiative - ERGA
Are all genes across human genome equally constraint?
No, some not conserved at all - ex brain size - other under a lot of constraint - measured by evolutionary conservation score phyloP - some human genes even lack evolutionary constraint
What is an example of human genome lacking evolutionary constraint?
Human accelerated regions (HAR) - excess mutations in humans - HARs located under human specific genes - ex: in the brain - cognitive abilities - HARs influence 3D organisation of proteins - enhances regulatory element binding - regulates human specific expression
What are HARs?
Human accelerated region (HAR) - sequences that changed little throughout mammalian evolution, but experienced a burst of changes in humans since divergence from chimpanzees
What is Anthropocene and why is it important?
Anthropocene - human-derived change - since 1950 new functionally and stratigraphically distinct geological epoch - black carbon, inorganic ash, fertilizers, pesticides, artificial radionuclides, increase in CO2, CH4, glibal temperature increase
Did rapid animal extinction begin in Anthropocene?
No, earlier - in holocene but after Homo Sapiens arrived in the Americas 14000 BCE - in XXist century 60% decline in populations - verall decrease in biodiversity
What are the reasons for major loss of biodiversity and population decrease on Earth?
Reasosn for decrease in biodiversity and populations:
- agricultural and urban development
- climate chnage
- poaching
How can genomics help with declining biodiversity and populations?
- Use ancient DNA to learn from what went extinct -
- Study current populations to see which populations need to eb prioritised
=> objective criteria for identification and analysis - identify species under threat - decide on conservation strategy
How can analysing ancient DNA help in conservation?
Can help establish genomic hallmarks of populations that are heading towards extinction - can compare:
- genetic diversity
- inbreeding levels
What are the two types of DNA samples used in sequencing?
- Modern DNA
- Ancient DNA - low quantity, low quality (fragmented), contaminated
What is the story of two mammoths?
Two mammoth aDNA sampels compared - one lived in larger earlier population (Oimyakon), the other in smaller dying isolated population (Wrangel) - comapred their genomes - genomic traces of uncoming extinction:
- lower genetic diversity
- higher inbreeding
What is an example of two populations which genomes can be compared to see the effects of conservation work
Gorillas - Grauer’s and Mountain gorillas experience critical population decline - but Mountain gorillas received conservation efforts (since 1970s?) but Grauer’s didn’t because die outside of their natural environments - compare past and current genomics - museum samples + field samples -> significant loss of genetic diversity in Grauer’s but stable in Mountain which were conserved by human efforts
What is the source of past genomic samples?
Museum animal spcecimens - scrape off DNA from skulls
What has to be considered in applying conservation work?
Need to objectively decide if conservation wrok needed - see genomics, populations + test after events which could influence
What genes experience high rates of mutations before species go extinct?
Increased mutation rates in essential genes - ex:
- immune response
- reproductive processes
Key points about genomics in conservation
Why we should sequence genomes of diverse organisms?
Explain what is metagenomics
Metagenomics - studies genetic material recovered directly from environmental / clinical samples by sequencing - contains genomes of many species
What are the environments where metagenomics can be studied?
Metagenomics studied environments:
- natural
- human-made
- host-associated
What are the benefits of studying metagenomics?
Study metagenomics to:
- understand how complex environments function
- discover new bioactive substances
- recognise changes in environment compositions to identify disease / seasonality / climate change / human-driven change
What are the main goals of metagenomic experiments?
Metagenomics aims to determine:
- what is in the sample - the species
- what are the functions - figure out functional profiles of enzymes, pathways
What is the workflow of a metagenomic experiment?
How is genome mapping performed in metagenomic experiments?
