Applied Molecular Genetics > Comparative genomics > Flashcards

Comparative genomics Flashcards

(52 cards)

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1
Q

what is comparative genomics

A

The comparison of intra- and interspecific genomic variation used to increase our understanding of evolution, genome structure, and the function of genes, encoded proteins, and non-coding regions

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2
Q

true/false comparative genomics is no longer limited to just subsets of the genome or less complex organisms

A
  • true
  • it used to be but w recent advancements in sequencing were good now
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3
Q

what are the 3 primary considerations in cmparative genomics

A
  • genome structure
  • types of structural change
  • evolutionary distance
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4
Q

describe the timeline of comparative genomics

A
  • 1980s comparatively small genomes: viruses + organelles
  • 1992 1st chromosome of yeast + large bacterial genome fragments
  • 1995 influenza full genome
  • 1996 eukaryote genome
  • ** 1999** multicellular eukaryote c elegans
  • 2002 human genome project 1st draft
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5
Q

what areas do comparative genomics aid in

A
  • evolution adaptive histories
  • disease/medicine/health genes involves or associated w disease resistance, risk, tolerance etc
  • Conservation Biology, Biotechnology, Agriculture, Biomolecular Structure & Function
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6
Q

what are some recent advances for comparative genomics

A
  • NIH have a comparative genomics resource
  • Multi-year national library of medicine (NLM) project
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7
Q

why does phylogeny mean

A

representation of the evolutionary history and relationships between organisms

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8
Q

what does monophyletic mean

A

a grouping of all organisms sharing a common ancestor

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9
Q

what is paraphyletic

A

a group od some, but not all, organisms sharing a common ancestor

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10
Q

what is polyphyletic

A

a group of organisms derived from more than one common ancestor

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11
Q

what do the diff colours mean

A
  • red monophyletic
  • blue polyphyletic
  • green paraphyltetic
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12
Q

what is a homolog

A

genes w a common ancestry

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13
Q

what is a paralog

A

divergence of homologous genes due to duplication

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14
Q

what is an ortholog

A

divergence of homologous genes due to speciation

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15
Q

what is synteny

A

2 genetic loci have been assigned to the same chromosome

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16
Q

what are the 2 types of synteny

A
  • collinearity
  • conserved synteny
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17
Q

what is collinearity

A
  • a type of synteny
  • that preserves the same order of genes on a chromosome from a shared ancestor (recent genomic usage)
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18
Q

what is conserved synteny

A
  • a type of synteny
  • the collection of orthologs within the same genomic region, regardless of order (recent genomic usage)
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19
Q

what is gene loss

A

when part of a chromosome is lost (ie deletion)

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20
Q

what is translocation

A
  • movement of genes de to genomic rearrangements
  • eg errors during recomb, where info from differing chromosomes are exchanges
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21
Q

how do we do comparative genomics

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A
  • strain
  • high quality genomic DNA
  • library prep
  • NGS
  • ne novo assemply
  • alignent on reference genome
  • genome finishing
22
Q

what does OrthoFinder do

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A
  • proteomic input data
  • complete set of proteins expressed by organism
  • relies on gene trees, so high accuracy
  • automatically process the date to infer…
  • the orthogroups for the species
  • rooted gene trees
  • rooted species tree
  • orthology relationships between the genes using the gene trees
  • geen duplication events
  • gives comparative genomic statistics for your species
23
Q

what does MOSGA stand for

Study These Flashcards
A

modular open-source genome annotator

24
Q

what is BUSCO score

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A
  • benchmarking universal single-copy orthologs
  • a measure of how complete a genome assembly is based on the presence of certain genes
  • > 95% is ideal
25
**true/false** BUSCO scores are applicable to both eukaryotes and prokaryotes
true
26
what is N50
- another way to measure quality of a genome assembly - based on size of contigs/scaffolds - half of the genome sequence is covered by sequences larger than or qual to the N50 size
27
**true/false** currently, OrthoFinder and MOSGA are the only tools/ethods for comparative genomics
false
28
what is the use of structural variants for comparative genomics
Relevant to both **evolutionary history** (and future) of our species, but also **disease**
29
**true/false** evolution in comparative genomics is basically phylogenetics
- **true** - Estimating relatedness between species in relation to observed sequence variation - Understanding evolutionary/adaptive histories that led to speciation events
30
what are conserved regions
- areas of high sequence similarity that has been preserved across distantly related organisms - generally linked to important biological functions - can help us find relatedness - *not limited to protein-coding regions*
31
what is an exaptation
- an ancestral gene that has been co-opted for a new function - parts of old genes genes are modified in order, components etc to provide a new phenotype
32
what is the therian sex chromosome system
X/Y
33
how can comparative genomics be used to understand the origin of behaviours
"Although comparative behavioral genomics cannot by itself tell us whether comparable behaviors in disparate species are similar by descent, this approach can help us more broadly identify appropriate model organisms for the interrogation of the epigenetic, molecular, and neural mechanisms underpinning particular behaviors"
34
what is salmonella
- one of the most common causes of bacterial foodborne infections worldwide - extensive host range - so very adaptable - comparative genomics can identify the genes responsible for virulency between hosts
35
what does COG stand for
cluster of orthologous genes
36
what is a core
identified across all serovars
37
what is a Vir-COG
virulence-associated COG
38
what are 2 key genes for salmonella that we care about
- **pegC** outer membrane protein - **iroD** enterochelin esterase *releases iron for bacterial metabolism*
39
why did we look at the comparative genomics of covid
- why is one strain more pathogenic than another - what modifications made it have higher transmisison rates - to what extent did the mutations happen and how likely will they happen in the future
40
what are nematodes and platyhelminths
- parasites - roundworms and flatworms respectively
41
what do nematodes and platyhelminths do
cause debilitating chronic infections of humans and animals
42
describe the comparative genomics they did of nematodes and platyhelminth
- looked at 81 genomes - 202 single copy orthologous proteins
43
what is a synapomorphic
- **a shared derived characteristic between organisms** - *comparing the change in the families, if the characteristics stayed the same or changed over time*
44
describe the drug thing they looked at
- identified new drug targets and new potential drugs - clustered compounds based on their molecular fingerprints - could see both overall number of compounds and the anthelminthic compounds
45
what is head and neck squamous cell carcinoma
5th most common non-skin cancer worldwide
46
what are the risk factors for head and neck squamous cell carcinoma
- exposure to tobacco + alcohol - infection w high risk HPV
47
why did they look at head and neck squamous cell carcinoma and what did they find
- common - no defined targetable geneic aberrations - no approved therapies tied to genetic alteations - discrepencies in understanding HPV + and - - neg tumors had unique genetic profiles, unique mutations
48
what is the link between knowing genes related to disease and medicine
- when we know the genes, we can design/modify human DNA to remedy these syndromes - like DiGeorge syndrome is caused by a gene deletion on chromosome 22 - can be caused by a mutation or inherited - symptoms can be severe - so maybe do gene editing to splice back the missing fragment
49
what are the negative impacts of doing gene insertions back into DNA in medicine
- Genotoxicity (while being inserted) - Gene silencing (after insertion) - Expression disruptions (after insertion) - Dysregulated cellular proliferation (after insertion; i.e. cancer)
50
what is GSH
- genomic safe harbor sites - regions of the genome where segments can be introduced without impacting typical cell function - can help w insertions cause we know the implications BEFORE altering the genomes
51
where can comparative genomics be applied beyond humans
- conservation bio - agriculture - biotech and biomolecules
52
Applied Molecular Genetics
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