…rapid growth rate …easy to modify genetically …features typical of eukaryotes …relatively simple (unicellular) …relatively small genome
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Sequencing the S. cerevisiae genome
Génolevure project
Euascomycetae
Neurospora
Loculoascomycetae
Laboulbeniomycetae parasites of insects
Basidiomycota rusts, smuts, mushrooms
Chytridiomycota Allomyces
The genome was sequenced by a highly cooperative consortium in the early 1990s, chromosome by chromosome (the whole genome shotgun approach was not used).
Monday Nov. 23: Eukaryotic genomes (Chapter 18) Wednesday Nov. 25: Eukaryotic genomes (Chapter 18) Next Friday: Thanksgiving
Monday Nov. 30: Hongkai Ji Wednesday December 2: Al Scott Friday: lab on eukaryotes
About 70,000 fungal species have been described (as of 1995), but 1.5 million species may exist.
Four phyla:
Ascomycota
yeasts, truffles, lichens
Hemiascomycetae
This involved 600 researchers in > 100 laboratories.
--Physical map created for all XVI chromosomes --Library of 10 kb inserts constructed in phage --The inserts were assembled into contigs
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Page 703
The EBI website offers a variety of proteome analysis tools, such as this summary of protein length distribution in S. cerevisiae.
Introns in ORFs:Байду номын сангаас220
Introns in UTRs: 15
Intact Ty elements: 52
tRNA genes:
275
snRNA genes:
40
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Features of the S. cerevisiae genome
A notable feature of the genome is its high gene density (about one gene every 2 kilobases). Most bacteria have about one gene per kb, but most eukaryotes have a much sparser gene density.
First species domesticated by humans
Called baker’s yeast (or brewer’s yeast)
Ferments glucose to ethanol and carbon dioxide
Model organism for studies of biochemistry, genetics, molecular and cell biology
These images and materials may not be used without permission.
Visit
Schedule
Monday: Yeast functional genomics (Jef Boeke) Wednesday: Fungi (Chapter 17) Friday: lab on yeast (start drafting your project!)
The sequence released in 1996, and published in 1997 (Goffeau et al., 1996; Mewes et al., 1997)
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Features of the S. cerevisiae genome
Sequenced length: 12,068 kb = 12,068,000 base pairs
Zygomycota
feed on decaying vegetation
Box 17-1 Page 699
Alternate classification of fungi
Outline of today’s lecture
Description and classification of fungi The Saccharomyces cerevisiae genome
Sequencing Features of the genome Yeast chromosomes Duplication of the yeast genome Functional genomics in yeast Comparative genomics of fungi
Introduction to fungi: phylogeny
Several criteria may be applied to decide if ORFs are authentic protein-coding genes:
Eukaryotic Genomes: Fungi
Wednesday, November 18, 2009
Genomics 260.605.01 J. Pevsner pevsner@
Copyright notice
Many of the images in this powerpoint presentation are from Bioinformatics and Functional Genomics by J Pevsner, copyright © 2009 by Wiley-Blackwell.
Length of repeats: 1,321 kb
Total length:
13,389 kb (~ 13 Mb)
Open reading frames (ORFs): Questionable ORFs (qORFs): Hypothetical proteins:
6,275 (see updates below) 390 5,885
Also, only 4% of S. cerevisiae genes are interrupted by introns. By contrast, 40% of genes from the fungus Schizosaccharomyces pombe have introns.
What are the most common protein families and protein domains? You can see the answer at EBI’s website: /proteome/
Fig. 17.1 Page 698
Classification of fungi
About 70,000 fungal species have been described (as of 1995), but 1.5 million species may exist.
Four phyla: Ascomycota
/proteome/
Fig. 17.3 Page 703
ORFs in the S. cerevisiae genome
How are ORFs defined? In the initial genome analysis, an ORF was defined as >100 codons (thus specifying a protein of ~11 kilodaltons).
Fungi are eukaryotic organisms that can be filamentous (e.g. molds) or unicellular (e.g. the yeast Saccharomyces cerevisiae).
Most fungi are aerobic (but S. cerevisiae can grow anaerobically). Fungi have major roles in the ecosystem in degrading organic waste. They have important roles in fermentation, including the manufacture of steroids and penicillin.
yeasts, truffles, lichens
Basidiomycota rusts, smuts, mushrooms
Chytridiomycota Allomyces