| |
D.
discoideum
|
T.
thermophila
|
S.
pombe
|
N.
crassa
|
|
Genome
|
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|
|
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haploid
chromosome #
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6
|
5
|
3
|
7
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size
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34Mb
|
200 Mb
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~14 Mb
|
42.9 Mb
|
|
fraction
sequenced
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~20%
|
~0.1% (dispersed)
|
~70%(expected
completion by end of 1999)
|
1%; funds awarded
to sequence ~30%
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|
genes/ORFs
|
10,000 (estimated)
|
~30,000 (from
hybridization)
|
~5,000 (estimated)
|
12.000 (estimated)
|
|
cDNA/EST
sequence
|
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Characteristics
|
|
|
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|
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cellular
organization
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simple multicellular
|
unicellular
|
unicellular
|
multicellular
(coenocytic)
|
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ploidy
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haploid/diploid
|
germline (transcriptionally
inactive) nucleus=2C; somatic (transcrip-tionally active) nucleus
~45C
|
haploid/diploid
|
haploid; a
brief diploid phase occurs between caryogamy and meiosis
|
|
generation
time
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4 hours (cell
->cell)
|
zygote->
zygote=1-14 days; cell-> cell, binary fission, 1.5 hr. minimum
|
~10 hrs. from
haploid ->diploid->haploid
|
sexual generation
time is ~14 days; cell division time in vegetative growth is ~140’
|
|
(egg->egg)
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3 days (spore->spore)
|
|
~2hrs to 3hrs
doubling time
|
N/A
|
|
cultivation
|
simple, inexpensive
|
simple, in
complex or defined media
|
|
simple, inexpensive
|
| |
|
|
|
|
|
|
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|
|
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transfection/transgenic
|
yes
|
yes; germline
or somatic only;
|
yes
|
yes
|
|
gene inactivation
|
homologous
recombination
|
gene knockout
and antisense
|
by homologous
recombination
|
Repeat-Induced
Point (RIP) mutations; reciprocal homologous integration
|
| |
|
|
|
|
|
mutants
|
many morphologicals
|
homozygous
recessive and dominant; large variety
|
many
|
~1,200 that
give rise to recognizable phenotypes
|
| |
|
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Cell Culture
|
|
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|
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Storage
|
|
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indefinite
storage of spores in fridge and cells in freezer
|
|
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gametes
|
N/A
|
N/A
|
N/A
|
N/A
|
|
embryos
|
N/A
|
N/A
|
N/A
|
N/A
|
|
intact organisms
|
indefinite
|
indefinite;
freezing; slow growing maintenance cultures
|
|
indefinite
at +4C if stored as conidia or mycelia; 10+years at +4 if stored
as ascospores
|
| |
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|
|
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|
| |
D.
discoideum |
T.
thermophila |
S.
pombe |
N.
crassa |
| |
|
|
|
|
|
Special Strengths
|
unicellular/multicellular;
large
scale screens;
excellent
cytology
|
Mendelian genetic transmission; homologous meiotic and somatic
recombination; excellent cytology; small introns; small amount of
repetitive DNA; natural host for human pathogens; functionally distinct
cilia; microtuble/dynein motility; microtubule heterogeneity; regulated
secretion; phagocytosis; cytokine-dependent growth; regulated sexual
maturation; related ciliate parasites
|
unicellular; defined colonies; haploid or diploid/ cheap, fast,
amenable to "classical" and "molecular" genetics
|
best understood filamentous fungus; densest genetic map, most identified
genes, most cloned genes, organized community; easy to grow; large
collection of mutants; closely related to important plant pathogens
and industrially important production organisms; molecular and regulatory
characteristics typical of higher eucaryotes.
|
| |
|
|
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Weaknesses
|
no specialized organs
|
unique genetic
code (TAA/G=GLN);
relatively small
research community
|
cytology difficult, but possible; limited development
|
no autonomously replicating vectors; multinucleate conidia; heterocaryotic
transformants; no stable diploids
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| |
|
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Resources
|
NICHD is providing funds to sequence the complete genome. This
is a three year grant and the support for the current year is ~$1.2M.
|
genetic maps of DNA polymorphisms; cDNA, cosmid and YAC libraries;
|
much information on genetics and cell cycle; ~70% of genome sequenced;
several culture collections
|
several culture
collections, cDNA, and genomic libraries available via Fungal Genetics
Stock Center;
two compendia describing all characterized chromosomal aberration
stocks and all mutants with observable phenotypes now in print and
being put on line; two fully searchable EST databases on the WEB;
genome being sequenced; biannual Newsletter focusing on new stocks
and techniques; all stocks available
|
| |
|
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Databases
|
DictyDB
Dicty.cmb.nwu.edu/dicty.html
|
Genetic Map Webpage;
http://lifesci.ucsb.edu/~genome/Tetrahymena
|
www.sanger.ac.uk;
www.bio.uva.nl/pombe/
|
The Perkins
et. al. compendia cross-referenced to genetic and molecular information
are being put on line, fully searchable genetic stock and molecular
biology technique and vector information is at
(http://www.kumc.edu/research/fgsc/),
fullysearchable EST databases exist at
(http://biology.unm.edu/~ngp/home.html
and
(http://www.genome.ou.edu/fungal.html)
and the WEB page for the Neurospora genome sequencing effort is
(http://fungus.genetics.uga.edu:5080/)
|
| |
|
|
|
|
| |
D. discoideum
|
T. thermophila
|
S. pombe
|
N. crassa
|
|
Community
|
|
|
|
|
|
# of labs
|
~150
|
~50 (mainly US, some in Europe and Japan)
|
>200 world-wide
|
~70 in US;~ 80 in rest of the world
|
|
# of investigators
|
492 on Dicty WWW server list
|
~200
|
>1,000 (estimate)
|
250 in US; 250 in rest of the world
|
| |
|
|
|
|
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# of investigators
|
492 on Dicty WWW server list
|
~200
|
>1,000 (estimate)
|
250 in US; 250 in rest of the world
|
|
References
|
Kuspa, A. and
Loomis, W.F. Ordered yeast artificial chromosome clones representing
the D. discoideum genome. PNAS USA 93:5562-5566.1996.
Maeda, Y.,
Inouye, K. and Takeuchi, I. [eds.] Dictyostelium.
A model system
for cell and developmental biology. Universal Academic Press: Tokyo,
Japan, 1997.
Parent, C.A.,
and P.N. Devreotes. Molecular genetics of signal transduction in
Dictyostelium. Annu. Rev. Biochem. 65:411-440.1966.
|
Asai, D.J and
J.D. Forney, eds. Methods in Cell Biology: Tetrahymena thermophila.
Academic Press, San Diego, CA In press (1999).
Coyne, R.S.,
D.L. Chalker, and M.C. Yao. 1996. Genome downsizing
during ciliate
development: nuclear division of labor through chromosome restructuring.
Annu. Rev. Genet. 30: 557-578.
Gall, J.G.
(1986). The molecular biology of ciliated protozoa (Orlando: Academic
Press, Inc.).
Frankel, J.
1989. Pattern Formation: Ciliate Studies and Models. Oxford University
Press, New York, NY.
Orias,E (1998):
Mapping the germ-line and somatic genomes of a ciliated protozoan,
Tetrahymena thermophila. Genome. Res. 8, 91-99.
Wheatley, D.N.,
L. Rasmussen, and A. Tiedtke. 1994. Tetrahymena: a model for growth,
cell cycle and nutritional studies, with biotechnological potential.
Bioessays. 16: 367-372.
|
Hoheisel et
al., High resolution cosmid and P1 maps spanning the 14 Mb genome
of the fission yeast S. pombe, Cell 73: 109-120 (1993).
Mizukami et
al., A 13 kb resolution cosmid map of the 14 Mb fission yeast genome
by nonrandom sequence-tagged site mapping, Cell 73: 121-132 (1993).
Nasim et al.
(eds.), Molecular Biology of the Fission Yeast, Academic Press,
1989.
Broach et al.
(eds.), Molecular and Cellular Biology of the Yeast
Saccharomyces
cerevisiae, Cold Spring Harbor Laboratory Press, 1991.
Alfa et al.
Experiments with Fission Yeast: A Laboratory Course Manual, Cold
Spring Harbor Laboratory Press, 1993
www.bio.uva.nl/pombe/handbook
|
Aramayo, R.
and Metzenberg, R.L. (1996) Meiotic transvection in fungi. Cell
86, 103-113.
Nelson, M.A.,
et. al..(1997) Expressed sequences from conidial,mycelial, and sexual
stages of Neurospora. Fung. Genet. Biol. 21, 348 -
363.
Perkins, D.D.,
et. al., 1982) Chromosomal loci of Neurospora crassa. Microbiol.
Rev. 46, 426-570.
Selker, E.U.
(1990) Premeiotic instability of repeated sequences in Neurospora
crassa. Annu. Rev. Genet. 24, 579 - 613.
Perkins, D.D.
Chromosome rearrangements in Neurospora. Adv. Genetics: 36. 239-399.
|
|
Information Provided By:
|
W. Loomis
|
M. Gorovsky
|
G. Smith; P. Nurse; B. Barrell; J. Sgouros
|
R. Metzenberg; J. Dunlap; M. Nelson
|
| |
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| 2/17/99 |
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