Biology 1002B Lecture Notes - Lecture 24: Tata Box, Comparative Genomics, Mycoplasma

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The Minimal Genome
1. What is the minimum set of genes needed to support independent cellular life?
2. How to identify which sequences are essential?
How many different chromosomes would you need to sequence to obtain the entire "human
genome"?
24, there are 23 pairs of chromosomes, 22 are autosomes
The 23rd pair is sex chromosomes, so need both X and Y because they are different
Genomic Analysis
1. Sequencing
2. Annotation
3. Functional Analysis
4. Evolutionary Analysis
Annotation: Where are the genes?
Where are the ORFs?
Annotating is finding the genes and parts and labelling them
There are 6 possible frames that the gene could be coded from double stranded DNA
o Find start and stop codon that is in frame that is about the right distance apart
o Find sequence that looks like promoter or TATA box
o Compare with other sequences that are already sequenced - use BLAST
Potential genes can be identified by
1. Computer searches for ORFs
2. Comparisons with know databases (BLAST searches)
Where are the genes in E. coli?
Genes are very tightly packed - very little space in genome
o Selective pressures for genomes to be small in prokaryotes, so little wasted space
Some genes are on one strand and other genes are on the other strand
o But the genes do not overlap
E. coli has high gene density compared to humans
o NOT because E. coli has more genes
o NOT because our genes are bigger
o Humans have defective mobile elements and viruses that takes up more than half of
our genome
Thus human genes are more spaced out
JCVI-syn3.0 (mycoplasma)
473 genes (438 protein coding)
Function of 149 genes remain unknown
Synthesized genome, smaller than any known free living microbe
Twice the size of minimal genome estimated by comparative genomics
Genes organized into functional groups
Minimum genes is under 500 in minimal genome!!
What is in your genome?
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