Fungal Genomes

genome

complete package of genetic material for a living thing

epigenome

up regulation and down regulation of genes

transcriptome

genes transcribed into RNA

Proteome

Peptide sequence

genomics

study of genes and their function, understanding the structure and fuction of the genome

classical genetics

• how genes line up on a chromosome

• gene function through mutations and mapping

Molecular genetics

• employs methods of genetics and molecular biology to find molecular function and interactions among genes

• look at structure and function of DNA, types/effects of mutation,and gene expression

loci

location on chromosome that is attributed to a function

Sanger sequencing

Produces long genomes

High-Throughput Sequencing Technologies

Creates short genomes

Higher Resolution

More detail when using a single marker for identifiation (ITS Regions)

Comprehensive View

Using information from thousands of genes provides a more complete picture of an organism’s evolutionary history

Gene alignment

Genes thought to be conserved across many fungi are identified, aligned and used to build a tree

Whole-genome alignment

By comparing whole-genome alignments, similarities can be assessed between species

K-mer analysis

Short, fixed-length sequences (k-mers) are counted and compared across different genomes to determine relatedness

Intra v interspecies differentiation

analyze whether the genetic variation within a species is lower than the cariation between different species

Shared polymorphism

Measuring the degree of shared genetic material that is inherited from a common ancestor can reveal how long ago species diverged

Genomic Markers for Fungal Phylogenetics

ITS, Ribosomal genes, protein coding genes, mitochondrial genes