21st Century Guidebook to Fungi, SECOND EDITION, by David Moore, Geoffrey D. Robson and Anthony P. J. Trinci

Table of Contents

1. Chapter 4: Hyphal cell biology and growth on solid substrates
2. Chapter 5: Fungal cell biology
   1. Mechanisms of mycelial growth
   2. The fungus as a model eukaryote
   3. The essentials of cell structure
   4. Subcellular components of eukaryotic cells
   5. The nucleus
   6. The nucleolus and nuclear import and export
   7. Nuclear genetics
   8. Mitotic nuclear division
   9. Meiotic nuclear division
   10. mRNA translation and protein sorting
   11. The endomembrane systems
   12. Cytoskeletal systems
   13. Molecular motors
   14. Plasma membrane and signalling pathways
   15. Fungal cell wall
   16. Cell biology of the hyphal apex
   17. Hyphal fusions and mycelial interconnections
   18. Cytokinesis and septation
   19. Yeast-mycelial dimorphism
   20. Chapter 5 References and further reading about the cell cycle
   21. Buy a PDF of Chapter 5
3. Chapter 6: Structure and synthesis of fungal cell walls

5.7 Nuclear genetics

The basic genetic architecture of fungi is fairly typical of the eukaryotes. Chromosomal structure and the nuclear division process are defining characteristics of eukaryotes, and all the major principles of genetics apply in fungi, namely gene structure and organisation, Mendelian segregations, recombination, and the rest (Moore & Novak Frazer, 2002; Dyer et al., 2017). Nevertheless, there are some differences between most fungi and other eukaryotes which we will highlight here.

Fungi have a generally smaller genome size than other eukaryotes (Table 2). Remember, though, that the higher organisms have much more non-coding DNA; for example in Homo sapiens, it is estimated that only 3% of the genome codes for protein.

Table 2. Approximate genome sizes of representative eukaryotes.
Organism	Genome size (Mb*)
Rhizopus oryzae	35
Saccharomyces cerevisiae	12
Aspergillus nidulans	31
Neurospora crassa	39
Coprinopsis cinerea	36
Ustilago maydis	20
Drosophila melanogaster	122
Sea Urchin	814
Human	3,300
*Mb = megabases (106 base pairs). Genomic data is held on open databases on the Internet which are freely available. For the most up to date details visit the following URLs: https://genome.jgi.doe.gov/programs/fungi/index.jsf https://www.ncbi.nlm.nih.gov/genome?term=txid4751[orgn]  https://www.ebi.ac.uk/genomes/eukaryota.html http://fungi.ensembl.org/index.html  http://fungalgenomes.org/ http://fungidb.org/fungidb/  https://en.wikipedia.org/wiki/List_of_sequenced_fungi_genomes  https://www.broadinstitute.org/fungal-genome-initiative

The Japanese pufferfish (Fugu rubripes) has the shortest genome known for any vertebrate species, being only one-tenth the size of the human genome, but the size difference between these two genomes can be explained by differences in intron sizes. In contrast, analysis of genomes of grasses reveals that differences in sizes (up to 40-times) can be explained by their having extensive regions between genes filled with repetitive DNA, suggesting that:

• in animals most repeats integrate into intron DNA,
• but in plants most repeats integrate into intergenic DNA.

The frequency of introns in the genome varies widely between different organisms. For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns; whilst introns are generally rare in the nuclear genes of yeasts. In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of yeasts may contain many introns (Freel et al., 2015). We might reasonably ask what are introns doing in the genome?

No-one can answer that question yet, though introns seem to have been a major evolutionary feature throughout the history of eukaryotes (Rogozin et al., 2012). The consensus seems to be forming that the exon-intron structure of protein-coding genes may have evolved as a protection against genetic instability that can result from transcription errors that damage the template DNA (Bonnet et al., 2017). The next Resources Box suggests a few articles that will give you a little more information about introns and topics for discussion and we describe fungal introns more fully in Section 18.6.

Resources Box What are introns all about? CLICK HERE to visit our page that provides access to references about introns. You can access the Wikipedia page about introns at this URL: https://en.wikipedia.org/wiki/Intron

Genomes are more similar when we compare the numbers of protein coding genes which the genomes specify. For example the Puffer fish and human genomes both contain about 30,000 genes (although estimates vary enormously), Drosophila melanogaster contains about 14,000; Neurospora crassa about 10,000 and yeast about 6,000.

The karyotype of most fungi, that is the profile of the chromosome set, can be resolved by electrophoresis (Wieloch, 2006). The technique reveals that chromosome length polymorphisms are widespread in both sexual and asexual species of fungi, revealing general genome plasticity. Tandem repeats, for example repeats of rRNA genes, frequently vary in length, and dispensable supernumerary chromosomes, which are usually less than one million base pairs in size, as well as dispensable chromosome regions also occur in fungal karyotypes. Many karyotype changes are genetically neutral; others may be advantageous in allowing strains to adapt to new environments (Mehrabi et al., 2017).

Updated January, 2020