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GENE221 > Lecute 19 > Flashcards

Lecute 19 Flashcards

1
Q

Genetics

A

Study of genes

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2
Q

Genomics

A

The study of genomes

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3
Q

Metagenomics

A

The study of all the genomes in a sample

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4
Q

What is a genome?

A

The total complement of genetic information of a cell or virus

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5
Q

Difference between Sanger sequencing and NGS

A

Sanger technology sequences one DNA fragment as a time using capillary electrophoresis

NGS allows massive parable sequencing using solid surface teachnology

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6
Q

Microbial genomic features of viruses

A
  • can be single or double stranded
  • non segmented or segmented
  • range from 1000nt to 250000000 nt
  • can contain envelopes
  • high mutation rates
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7
Q

Microbial genomic feature of bacteira

A
  • double stranded DNA
  • usually circular
  • usually one chromosome
  • size range form 1-14 minion nt
  • can contain plasmids
  • slow mutation rates
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8
Q

What is genomics

A

The discipline involving the mapping sequencing and analysis of genomics

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9
Q

Microbial and comparative genomics - 4 steps to get from determining the genome sequence to understanding what it means

A
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10
Q

Two types of DNA sequencing

A

Sanger sequencing

Next generation sequencing
- short read technology (illumina)
- long read technology (oxford)

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11
Q

Next generation sequencing - iliumiina sequencing

A
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12
Q

Long vs short reads - oxford nanopore and illumina

A

Main difference is that long generates long reads and short generates short read

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13
Q

Main downfall of short rads in next gen sequencing

A

You may miss gaps - sequence gaps in short reads

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14
Q

Main downfall of short rads in next gen sequencing

A

You may miss gaps - sequence gaps in short reads

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15
Q

What kind of next gen sequencing are used for viscoses

A

Short reads as their RNA is rapidly degradable

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16
Q

Once all the short reads are sequenced what must happen?

A

Assembly to make a long sequence

17
Q

How do u do gene annotation - like knowing what part of the genome belongs to each gene or protein

A
  • using a selection of automated tools
18
Q

Automated genome annotation vs manual genome annotation

A
  • automated genome annotation is fast/consitant
  • manual annotation can add value as wont miss anything
19
Q

Are people needed to interpret the genome data?

A

Yes

20
Q

genome data interpretation

A
  • people are needed to interpret the data and compare this to the biology of the organism
  • genes present in genome can determine the biology of that organism
  • conversely the biology or niche inhabited by an organism can determine its genome content
  • host genetics play a huge role in a virus’ ability to adapt to a new host
21
Q

Genome data interpretation - SARS-CoV-2 spike example

A
  • the genome of SARS-CoV-2 includes a gene that encodes the spike protein
  • changes in the RNA sequence of that spike protein results in changes in the shape of the spikes structure
  • its spike changes all the time to invades to immunity we have from past infections and vaccines
    = it changes at a fast rate in order to survive
22
Q

What two things can sequencing genome data tell us?

A
  • what is there
  • how much of it there is
23
Q

What does interpreting the genome data amount show us?

A
  • can estimate the relative abundance of sequence reads
  • this corresponds to an organisms abundance or gene expression
  • read abundance can tell us a lot about genetic function
  • how many reads per contig?
24
Q

What is comparative genomics

A

Comparative genomics is the comparison of genome strucuture and function across different biological species or strains

25
Q

What does comparison of genomes provide?

A
  • comparison can aid in identifying differences
  • the regions of difference can help identify genes involved in a particular process
  • close comparisons (microevolution)
  • distant comparisons (macroevolution)
26
Q

Cmparision it’s important in identifying a….

A

Novel emerging pathogen

27
Q

What is comparative genomics

A

The comparison of genome structure and function across different biological species or strains

These techniques can provide valuable insight into the biology and evolution of microorganisms

GENE221 (23 decks)

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