5.7 Nuclear genetics

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 External Resources Box suggests a few articles that will give you a little more information about introns and topics for discussion.

  • in animals most repeats integrate into intron DNA,
  • but in plants most repeats integrate into intergenic DNA (Wong et al., 2000).

So we might reasonably ask what are introns doing in fungi? No-one can answer that question yet, unless they are left over from the universal ancestor (see the section The tree of life has three domains in Chapter 2; CLICK HERE to view it now). The next Resources Box suggests a few articles that will give you a little more information and discussion.

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; Neurospoa 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 July, 2018