genomics of A. gambiae Flashcards
1
Q
genome assembly
A
- raw genome sequence not useful for linking genotype to phenotype
- don’t get whole genome readout all at once
- sets of short/long reads
- can come together without or with gaps of predicted size depending on system
- need to assemble reads into a library
2
Q
assembling reads into libraries
A
- extend and connect reads → contigs
- connect contigs → scaffold
- current final state of genome sequencing
- ultimate goal will be to assemble whole chromosome
- more repetitive DNA makes assembly difficult and affects scaffold length
3
Q
genome ‘homes’
A
- place to share genome information for other researchers to build on
- VectorBase → disease vector genomes
- gene structure, expression date, orthology information, protien domains, population domain
- identified by in silico algorithms
- open access → correct/improve annotation errors
4
Q
anchoring
A
- anchor genomic data to RNAseq data
- improves annotation
- if mapping isn’t the same, can improve predictions
- expression data form multiple samples
- indicates function in different tissues, sexes, populations, feeding
- confirmed by statistical data
5
Q
orthology
A
- use of data from closely related organisms
- homologue = common ancestry of 2 or more genes
- orthologue = homologous genes in multiple species
- paralogue = 2 genes in 1 species from a single ancestor
- requires a duplication event
6
Q
Dorsal gene
A
- ancestral Drosophila gene
- in embryogenesis and immunity in adults
- Rel1 in Anopheles
- 2 genes in Aedes
- couldn’t manage both roles
- duplicate to overcome → one for early role, one for later role
- expression of one gene spikes early and never again
- paralogues
- orthologues of Dorsal/Rel1
7
Q
observations in mosquito immunity to malaria
A
- strongest bottleneck in mosquito stages
- is this the mosquito immune system?
- refractory Anopheles species exist in nature
- map susceptibility to genome?
8
Q
identification of mosquito immune-like genes that determine malaria susceptibility
A
- team at EMBL
- used 3 techniques
- comparative genomics
- expression data with microarrays
- infected vs. non-infected
- now RNAseq
- RNAi knockdown to confirm roles of genes
- identified TEP amplification
9
Q
TEP
A
- thioester-containing proteins
- family of proteins highly amplified in mosquitoes
- 15 copies in A. gambiae, 1 in Drosophila
- duplication to combat infection?
10
Q
TEP16
A
- originally thought to be separate gene from TEP1
- actually alternative allele of TEP1
- cross S strain (TEP1) with strain R (TEP16)
- offspring are heterozygous TEP1/TEP16
11
Q
strain R
A
- built on refractory individuals - Tep1r
- RNAi studies to knockout
- control → almost 0 oocysts in midgut
- knockdown → normal distribution of oocytes/midgut vs percentage of mosquitoes
12
Q
strain S
A
- built on susceptible mosquitoes - Tep1s
- RNAi knockout:
- control with lacZ injection → normal distribution of oocytes/midgut vs percentage of mosquitoes
- knockdown → increased infection (shift to the right)
13
Q
alternative alleles
A
- phenotype of malaria susceptibility depends on the allele present
- why has susceptible allele not been selected against?
- adaptation to specific niches
14
Q
Tep allele distribution
A
- in africa, distribution of alleles among M and S forms is highly variable
- M (coluzzi) and S (ss) chromosomes are very different so that they can occupy different niches
- peak in allele diversity in chromosome 3 that overlaps Tep1 gene
15
Q
Tep in S and M forms
A
- 2 forms of Tep1r allele
- A and B
- M form almost completely resistant
- genetic sweep of rB in M only
- but not in all populations, and no sweep in S
- some M form still susceptible and act as vectors, as well as S
- selective pressure may not be plasmodium infection, meaning that rB does not always confer survival advantage
- something else e.g. habitat
- selective pressure may not be plasmodium infection, meaning that rB does not always confer survival advantage
