What is the genome of an organism?
whole hereditary information of an organism encoded in the DNA (or RNA for some viruses)
includes genes and non-coding sequences.
Who first coined the term "genome" and when?
Hans Winkler (1920) in Hamburg, Germany
What are different genetic materials in a cell?
complete set of nuclear DNA (nuclear genome)
mitochondrial genome
chloroplast genome
Briefly describe Pro- and Eukaryotic cells
Prokaryotic:
—> smaller, no nucleus, single circular DNA molecule
Eukaryotic:
—> larger, nucleus, multiple linear DNA molecules
What was the first viral genome to be sequenced and when?
bacteriophage MS2 in 1976, consisting of 3,569 base pairs
What is the range of genome sizes in bacteria and archaea?
Bacterial: 0.5 - 13.2 Mb
Archaeal: 0.5 - 6 Mb
How many nucleotides are there in the human nuclear genome?
~3.2 billion
What is the structure and size of the human mitochondrial genome?
circular DNA molecule of 16,569 nucleotides
How does the process of DNA sequencing using terminator bases work?
DNA polymerase copies strand of DNA
nsertion of terminator base —> halts the copying process
—> resulting in fragments of different lengths.
fragments separated by size
fluorescent label the terminator bases —> computer reads sequence.
What is the difference between clone-by-clone shotgun sequencing and whole-genome shotgun sequencing?
Clone-by-clone shotgun sequencing
mapping
sequencing overlapping clones
Whole-genome shotgun sequencing
skips mapping phase
sequences entire genome in parallel
—> followed by computational assembly
What are some applications of genome sequencing in modern science?
novo sequencing
ancient DNA studies
metagenomics
resequencing
somatic mutation analysis
transcriptome analysis
epigenetics
Does the genome size directly correlate to the number of coding genes in an organism?
No, it does not, see table
Does complexity of an organism correlate with the number of genes in its genome?
No!
e.g some simpler organisms may have more genes than more complex organisms. (A.thaliana)
What are LINEs and SINEs and what differentiates them?
types of repetitive DNA sequences found in eukaryotic genomes
LINEs (long interspersed nuclear elements)—> longer
SINEs (short interspersed nuclear elements) —> shorter, often derived from tRNA sequences
What are some key elements analyzed in computational genomics? (Name some)
genome sequence and variations
genomic strucutres
protein-coding genes
RNA-coding genes
pseudogenes
homologs/orthologs/paralogs
promoters/terminators
regulatory elements
transposable elements
Name the most important databases for genomic information
JGI
UCSC
Ensembl
Name a database for viral genomes like CoV-19
GISAID
Describe the main components of a eukaryotic genome
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