TU Genomes and genomics of Aspergillus

Question 1

Aspergillus niger

Answer 1

• industrial fungus used for production citric acid and enzymes.
• 8 chromosomes, 30-36Mbp
• The life cycle of A. niger is primarily asexual, with black conidiospores that are commonly used as a distinguishing feature.
• The asexual life cycle: spores (conidia) -> swollen conidia (happens in the right surroundings/conditions) -> gemination into germlings -> mycelium -> Conidiophore Formation ->
  Sporulation (Conidia Formation)

Question 2

Parasexual Cycle in Aspergillus niger

Answer 2

A. niger lacks a known sexual cycle, so a parasexual cycle is used for genetic crosses.

• diploid genome -> haploid genome. Forced haploidization using microtubule destabilizing drug (benomyl),
• Analyze haploid progeny for segregation of the desired phenotype and identify linked mutations.
• During the diploid stage, genetic recombination can occur between homologous chromosomes, which wouldn’t happen in haploids. This helps to shuffle the genome and produce new traits or phenotypes.

Question 3

Mutation Identification Strategies

Answer 3

Backcrossing: breeding method, used to introduce or retain a specific trait while maintaining the overall genetic makeup of the parent strain (By backcrossing you keep crossing parent and mutant strain until the mutation you want is the phenotypic trait left)
-> you can introduce the disease-resistance trait from the donor parent into the high-yielding crop over several generations, while still maintaining the high-yield trait of the recurrent parent.

Complementation analysis: determines whether two mutations that produce the same phenotype (usually a defect) are in the same or different genes by crossing individuals and observing the phenotype of their offspring
* If the offspring display a wild-type (normal) phenotype, the mutations are likely in different genes, meaning the mutations complement each other, the mutation gets overwritten by the other healthy gene. If the offspring still exhibit the mutant phenotype, the mutations are likely in the same gene -> non-complementation

Question 4

Mutation Identification Strategies: Segregant analysis

Answer 4

Segregant analysis looks at inheritance patterns across generations by examining individual offspring rather than pooled samples

Bulk Segregant Analysis (BSA) a technique used to identify genetic markers associated with a mutant phenotype by pooling individuals from different groups (such as those exhibiting and those lacking a specific trait). The pooled DNA is then sequenced to identify genetic markers like SNPs linked to the trait. This helps narrow down specific genomic regions associated with the phenotype of interest.

Process segregation:
1. Cross the mutant strain with a wild-type strain and obtain a large number of progeny. Pool the progeny showing the phenotype of interest and sequence their DNA.
2. Detirmine SNP’s between parents
3. Determine SNP’s in the mutant pool
a) SNP’s not linked to phenotype: two alleles present in the sequencing data of mutant pool
b) SNP’s linked to phenotype: one allele present in sequencing data of mutant pool
(Compare the pool sequence with the wild-type sequence to identify shared single nucleotide polymorphisms (SNPs) and mutations linked to the trait)