Lecture 19 Flashcards
define genome
is the full halpoid set of dna sequence in an organism
- How can genomes inform us about gene function?
we can sequence genomes to separate them into reads and learn about the individual genes and compare them to full genome
- How can genomes inform our understanding of evolutionary relationships?
- How can genomes inform our understanding of unculturable bacteria?
even though we cannot grow the bacteria ourselves in the lab we can sequence gthe genomes of these unculturable bacteria and determine the genes that allow it to grow in its environment.
- What is clone by clone sequencing? How is it different from shotgun sequencing?
- chromosome of are fragmented using partial restriction digest to create overlapping fragments
- the chromosome fragment clone into BAC vector
- the vector is sub clones into small fragments
- fragments assembled into large fragments by computer
shotgun sequencing:
1. break gDNA into small fragments
2. computer assembles overlapping sequences and the gaps of sequencing can be determining
Compare and contrast short and long-read sequencing technologies. What are the advantages and
disadvantages of each?
long reads: allows for longer reads more expensive , but higher error rate
(pAC-BIO, OXFORD NANOPORE)
short reads sequencing: lower error rate
- What is a GWAS? Does it entail assembling a genome? Why or why not?
GWAS: invovles sequencing individuals with gene of interest and those without gene of interest using short read sequencing ( Illumina) and map these short reads on the reference genome
you will then look for variants that correlated with diseases genes
You do not need to assemble each individuals genome
Design an evolve and resequence study for antibiotic resistance genes in a species of pathogenic
bacteria. What would you look for in the sequencing data to determine if a gene was causal?
continuous culture with chemossta and monitor for bacterial growth on the antibbiotic plate. These are the evolved f2 cell line that are antiobiotic resitance able to grow on antiobiotic plate due to the chemostat allowing for natural selection of cells.
Therefore if they have a mutation compared to the f1s that are not able to grow on the antibiotic plate that mutation is adaptive
chemostat allows you to constantly put new media while removing old media for yeast to grow in.
Adaptive mutation to produce sulfate in sulfate limited conditions will arise.
you then sequence evolved lines and the ancestors and identity if mutations the evolved line has that the ancestor does not.
you then identify in replicatates if the same mutation is happening over and over again; if so the change is adaptive
What can be inferred based on the differing results in the two yeast species evolved in sulfate
limited conditions described in lecture? What is a chemostat?
based on the different results in the two yeast species it was determined that duplicating sol1 gene has a large affec on fitness in cerevisiae opposed to uvarum whereas mutations to sol2 did allow the uvarum to produce sulfur in sulfate limited conditions.
Therefore sequence gave us information that sol 1 and sol2 which are both sulfur producing genes use different transport mechanisms to produce sulfur
What species were sequenced in the human genome project? What method did they use?
they used the clone-by-clone methodology and other species such as drosophila, c.elegans, e.coli, saccharomyces cerevisiae, mus musculus
- What is the great plate count anomaly and what explains it?
The great plate count anomaly the number of colonies that appear when plating cells is FAR less than the actually number of cells present—> most bacteria is not culturable
What is the Baas-Becking hypothesis? How would a change in microbiome following a dietary
change be explained by the Baas-Becking hypothesis?
bass-becking hypothesis: natural selection is the most power force affects microbial ecology
the change of environment selects for bacteria that are best fit to survive in the environment however those bacteria can colonize all environments
the gutmicrobiome changes based on the diet an envrioinemt with a certain diets will select for the best fit micrbiomes to survive
Contrast structural annotation and functional annotation. How can genes be identified in a
sequence? What is a drawback to this method?
structural annotation:
locating the gene
can locate the gene based on if it has greater than 50 AAs however a drawback is that you would miss some coding genes that have less than 50 AAs.
sequences must be scanned in 6 different ways as there are 6 different reading frames ( 3 reading frames in each direction)
functional annotation:
to understand the function of identified function can
- by looking at the domain of the gene you can determine its function
Some functions can be understood simply by sequencing the genome and analyzing across species if there are similarities in sequence. You can then infer that they have the same function.
structural mutations can result
What is the core genome of a species? What is the pangenome of a species?
Pangenome: all genes present in a species
core genome: genes shared by all individuals of a species
What is the C-value paradox and what explains it?
organismal complexity does not correlate to genome size
genome size is not indicative of complexity as size is typically indicate of the amount of noncoding transposable elements in the genome
