MO Genomics of yeast

Question 1

Saccharomyces cerevisiae

Answer 1

• baker’s yeast
• is either haploid (one chromosome) or diploid (two chromosomes)
• Its relatively small genome (12.3 million base pairs with approximately 6,571 genes)
• first eukaryotic genome to be fully sequenced in 1996
• a big part of chromosomes/genomes in eukaryotes are non coding (no ORF’s)

Question 2

Yeast Genome Sequencing and Nomenclature

Answer 2

• ORFs (open reading frames) are the fundamental coding elements identified within the yeast genome, ORF is a section of DNA that starts with start codon and ends with stop codon withot interruptions.
• The yeast genome is organized into 16 chromosomes with a specific nomenclature for example, YDR130c indicates
  Y refers to Yeast.
  D refers for Chromosome IV.
  R indicates Right arm of the chromosome.
  130 indicates that this ORF is the 130th gene from the centromere on that arm.
  c/w Indicates whether the ORF is on the Crick (c, Tamplate) or Watson (w, coding) strand.

Question 3

Different genes

Answer 3

Gene duplication is a crucial source of genetic diversity in yeast, producing gene families with related functions.
Key terms associated with gene duplication in yeast
* Orthologs Genes in two separate species that evolved from a common ancestral gene in the last shared ancestor. providing the same function
* Paralogs Genes that are duplicated within a single genome and then evolve independently in the same organism, different gene functions
* Homologs A broader category including both orthologs and paralogs, referring to genes related by descent.

Question 4

Industrial and Ecological Applications of Yeast

Answer 4

• Domestication of yeast strains for industrial applications has led to significant genetic divergence from wild strains.
• Industrial yeasts, The brewing yeast Saccharomyces pastorianus is a hybrid species with a complex genome composed of two nuclear subgenomes from S. cerevisiae and S. bayanus make well-suited for lager brewing.

Question 5

Antisense Transcription

Answer 5

• regulates gene expression by transcribing asRNA from the opposite antisense/ coding strand of DNA, which can inhibit sense transcription. As it is the mirror image of mRNA, allowing it to hinder mRNA function.
• antisense transcription results in deacetylation of histones in the promoter for sense-transcription, resulting in inhibition of sense-transcription

Question 6

Genome-wide RNA-Seq Analysis

Answer 6

• Volcano plots were used to visualize upregulated and downregulated genes at three time points (45, 120, and 200 minutes), showing how gene expression patterns change in response to stress.
• Venn diagrams were used to display overlaps in differentially expressed genes across the three time points, highlighting genes that are persistently regulated and those that show transient expression patterns.

Question 7

Aneuploidy

Answer 7

Aneuploidy a yeast cell has abnormal number of chromosomes, either missing chromosomes (hypoploidy) or extra (hyperploidy), deviating from the normal set of 16 chromosomes in Saccharomyces cerevisiae.
Aneuploidy can occur naturally or under stress conditions, and it often leads to altered gene expression, affecting the cell’s physiology