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Lecture 5

Biology 2581B Lecture Notes - Lecture 5: Densitometry, Microsporidia, Ribosomal Rna


Department
Biology
Course Code
BIOL 2581B
Professor
David R Smith
Lecture
5

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Lecture 5: Genome Diversity - Size
- genomes exist in:
nuclei
chloroplasts
mitochondria
bacteria
archaea
viruses
- genome: a set of genetic instructions within a biological compartment
- genome size: the length of those instructions
Units of Genome Size:
- length:
-1 base pair (bp) = A-T or G-C
-1000 base pairs => kilobase (kb)
-1,000,000 base pairs => metabase (Mb)
-1,000,000,000 base pairs => gigabase (Gb)
- mass:
-1 billion bp =1 pg (picogram) in mass
-haploid human nuclear genome:
-mass ~3 pg
-length is ~3 billion bp (~3 Gb)
Measuring Genome Size:
sequence and assemble genome:
-once it’s assembled, can determine the size
-example:
grow polytomella in a culture
spin to make a pellet
use a kit to isolate the DNA
send DNA to sequencing centre
spits out millions of little sequences of DNA
can order them on a computer
-if there was a pure sample, would be nuclear genome, mitochondrial genome, but for
polytomella no chloroplast genome
-sequences are established in many fragments that are lined into contigs in regards to
overlap
-this types of sequencing is not good for big genomes:
lots of repeats, so computer gets confused
too much data for basic computers to deal with
even though millions of reads, not enough to piece together entire chromosomes
staining and imaging:
-wash cells in DNA stain
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-under a microscope connected to a computer, look at stained chromosomes
-intensity of pixels is related to genome size
-it would matter if the nucleus was haploid or diploid
-stain would be 2x as intense
-“Feulgan Image Analysis Densitometry”
gel electrophoresis:
-DNA migrates across a gel based on size
-compare to a known set of references in the adjacent well
-not great for very large genomes, but good for small ones
DNA flow cytometry:
-stain a DNA and measure level of fluorescence
-good for big genomes
Exploring Genome Size:
-initially, determined that tinier organisms had small genomes, while large, complex organisms
had larger genomes
-compared across different domains
-within a single domain, there is a lot of variety
-genome size has no relation to complexity
- C-value paradox: discordance between complexity and genome size
-(C-value refers to the genome size )
-one of the biggest genomes belongs to the marble lungfish => 130 billion bp
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