| |
S.
cerevisiae
|
C.
elegans
|
D.
melanogaster
|
D.
rerio
|
X.
laevis
|
|
|
|
|
|
|
|
Genome
|
|
|
|
|
|
|
haploid
chromosome #
|
16
|
6
|
4
|
25
|
18
|
|
size
|
12 Mb
|
97 Mb
|
165 Mb
|
1700 Mb
|
~ 3000 Mb
|
|
fraction
sequenced
|
100%
|
>99%
|
~15%
|
< 1%
|
< 1%
|
|
genes/ORFs
|
6217
|
19,099
|
12,000-15,000
|
|
50-70,000
|
|
cDNA/EST
sequence
|
|
~68,000 ESTs
from ~7,400 genes
|
|
~10,000
|
|
| |
|
|
|
|
|
|
Characteristics
|
|
|
|
|
|
|
cellular
organization
|
Unicellular
|
multicellular
|
complex multicellular
|
complex multicellular
|
complex multicellular
|
|
ploidy
|
Haploid/diploid
|
diploid
|
diploid
|
diploid
|
tetraploid
|
|
generation
time
|
|
|
|
|
|
|
(egg->egg)
|
hours
|
3 days
|
~12 days
|
3 months
|
1 year
|
|
cultivation
|
simple inexpensive
|
simple inexpensive
|
simple inexpensive
|
more complex,
|
simple, requires
space
|
|
|
|
|
requires space
|
|
| |
|
|
|
|
|
|
transfection/transgenic
|
yes
|
yes
|
yes
|
yes
|
yes
|
|
gene inactivation
|
homologous
recombination
|
RNAi, transposon
insertion
|
transposon
insertion, RNAi,
|
transposon
insertion
|
|
|
|
|
chem. and
X-ray mutagen.
|
|
|
|
mutants
|
many
|
many
|
many
|
>7,000
|
|
|
|
|
|
|
|
|
Cell Culture
|
yes
|
no
|
yes
|
yes
|
yes - from
tadpole stages
|
|
|
|
|
|
|
|
Storage
|
|
|
|
|
|
|
gametes
|
N/A
|
|
|
sperm yes;
eggs +/-
|
|
|
embryos
|
N/A
|
|
for archival
storage
|
|
|
|
intact organisms
|
indefinite
as stabs & glycerol
|
mos at +11C;
indefinite at -196C
|
|
|
|
| |
stocks
|
|
|
|
|
|
Special Strengths
|
Unicellular
|
small number of cells
|
sophisticated genetics
|
transparent
|
early embryogenesis
|
| |
Haploid/diploid
|
cell lineages completely known
|
polytene chromosomes
|
early embryogenesis
|
larval metamorphosis
|
|
large scale screens
|
neuronal connections all known
|
wealth of mutants
|
assay phenotype in
|
easy assay of transcripts by
|
| |
homologous recombination
|
neurons have simple structure
|
much info. on evolutionary,
|
haploid embryos
|
RNA injection
|
|
|
|
quant., and pop. genetics
|
|
biochemistry
|
| |
|
|
devel.
reg. well understood |
|
|
|
|
|
2-component
Gal4 system |
|
|
| |
|
|
biochemistry
|
|
|
|
|
|
|
|
|
|
Weaknesses
|
unicellular
|
no cell culture
|
embryo freezing impractical
|
genomic resources just
|
no RNAi or homol. recomb.
|
|
difficult cytology
|
no homol. recomb.
|
no homol. recomb.
|
developing
|
tetraploid
|
| |
|
|
|
no
RNAi or homol recomb. |
|
|
|
|
|
|
|
| |
|
|
|
|
|
|
Resources
|
complete genome sequence
|
nearly complete genome sequence
|
stock centers
|
stock center just
|
EST library of unfert. eggs
|
| |
genome wide k.o. in progress
|
stock center
|
cDNA, genomic, 2-hybrid
|
developing
|
|
|
genome wide 2-hybrid in
|
e.m. resource
|
libraries available
|
|
|
| |
progress
|
pilot project on gene k.o.'s
|
|
|
|
|
stock
center |
|
|
|
|
| |
|
|
|
|
|
|
Databases
|
SGD
|
ACeDB
|
Flybase
|
ZFIN
|
web pages:
|
| |
genome-www.stanford.edu/
|
elegans.swmed.edu
|
flybase.bio.indiana.edu
|
zfish.uoregon.edu/ZFIN/
|
www.ahsc.arizona.edu/uac/
|
|
Saccharomyces/
|
|
|
|
iacuc/xenopus/xenopus
|
| |
|
|
|
|
www.cshl.org/books/
|
|
|
|
|
|
xenopus html
|
| |
|
|
|
|
AXelDB database of partial
|
| |
|
|
|
|
seq
& in situ patterns-neurula |
| |
|
|
|
|
|
| Community
|
|
|
|
|
|
|
# of labs
|
124 in SGD
|
~300
|
~1,000
|
198 in ZFIN
|
|
|
# of investigators
|
|
~1,200
|
5-10,000
|
1739 in ZFIN
|
|
| |
|
|
|
|
|
| |
|
|
|
|
|
| |
|
|
|
|
|
| |
|
|
|
|
|
|
References
|
Broach JR, Pringle JR, Jones
|
Epstein HF, Shakes DC, eds.
|
Roberts DB: Drosophila: A
|
Westerfield M: The Zebra-
|
Amaya E, Offield MF, Grainger
|
|
EW: The Molecular & Cellular
|
Caenorhabditis elegans. Academic
|
Practical Approach. IRL
|
fish Book. University of
|
RM: Frog genetics: Xenopus
|
| |
Cold Spring Harbor Press, 1991
|
Chalfie M, Jorgensen JM: C. elegans
|
Ashburner M: Drosophila: A-
|
|
|
| |
Saccharomyces cerevisiae.
|
|
|
line at ZFIN)
|
TIG 14: 253, 1998
|
| |
Cold Spring Harbor Press, 1991
|
Chalfie M, Jorgensen JM: C. elegans
|
Ashburner M: Drosophila: A-
|
|
|
| |
|
neuroscience: Genetics to genome.
|
Laboratory Handbook. Cold
|
Zebrafish Issue of
|
|
| |
Rose AH, Wheals AE, Harrison
|
TIG 14: 506, 1998
|
Spring Harbor Press, 1989
|
Development v. 123, 1996
|
|
| |
JS.
The Yeasts. 2nd ed, |
|
|
|
|
| |
Academic Press, 1995
|
C. elegans Sequencing Consortium:
|
|
|
|
| |
|
Genome
sequence of the nematode |
|
|
|
| |
Chervitz et al: Comparison of the
|
C. elegans, A platform for investiga-
|
|
|
|
| |
complete protein sets of worm
|
tional biology. Science 282: 2012,
|
|
|
|
| |
and yeast: orthology and
|
1998
|
|
|
|
| |
divergence.
Science 282:2022, |
|
|
|
|
| |
1998
|
Wood WB, ed. The Nematode
|
|
|
|
| |
|
C.
elegans. CSH Press, 1988 |
|
|
|
| |
Spellman et al: Comprehensive
|
|
|
|
|
| |
identification of cell cycle-regu-
|
Riddle DL, Blumenthal T. Meyer BJ,
|
|
|
|
|
|
lated genes of the S. cerevisiae
|
Priess JR, eds. C. elegans II.
|
|
|
|
| |
by microarray hybridization.
|
CSH Press, 1997
|
|
|
|
|
|
Mol. Biol. Cell 9:3273, 1998
|
|
|
|
|
| |
|
|
|
|
|
|
Current
NIH Funding Related to NCI Working Group Recommendations
(Not comprehensive; information provided by NIH Staff)
|
S1.B.iii. Cellular
localization of proteins: NCI funds 1 grant for pilot project ($1.5M
over 3 yrs)
S1.B.v. Use
of array technology to study cellular processes at genome-wide level
: NHGRI funds 1 grant ($4.5M over 3 yrs)
|
S.2.B.i. Genomic/gene
sequence of C. briggae: NHGRI supports 1 grant to seq genes &
limited ESTs from distantly related nematodes ($2M over 3yrs)
S. 2.B.ii.
Knock-outs: NHGRI funds 1 pilot project to KO 2000 genes ($1.4M
over 3yrs)
|
S.3.B.i. Seq
full-length cDNAs: NHGRI&DOE co-fund transcriptional mapping
of ESTs from 9,000 full-length cDNAs ($0.8M over 3 yrs)
S.3.B.ii. Knock-outs:
NHGRI & NCI co-fund P element insertional mutagenesis for controlled
misexpression of genes on 2nd chromosome ($0.7M over
3 yrs)
|
S.4.B.i. 2
cM microsatellite map: Multi-Institute support of: 1 grant to generate
1.3 cM map using microsatellite markers, 1 grant to generate meiotic
map of 500 SSLPs and 2800 gene-based markers. ($6.2M over 3 yrs)
S.4.B.ii EST
seq & full-length cDNAs: Multi-Institute support to seq 50K
ESTs and map 5K ESTs onto RH panel ($7.0M over 3 yrs)
S.4.B.iii.
Infrastructure/genetic techniques: NHGRI & NCRR support 2 grants
for insertional mutagenesis ($0.95M/yr); NCRR, NIDDK, NICHD &
NCI support stock center for wildtype and mutant zebrafish and cryopreserved
sperm ($1.3M/yr; 5 years)
|
|
| Table
Created by David Valle with Additional Information from: |
Ira
Herskowitz |
Geraldine
Seydoux, Robert Herman, Ira Herskowitz |
Daniel
Hartl, Thomas Kaufman, Gerald Rubin, Ira Herskowitz |
William
Talbot, John Postlethwait, Ira Herskowitz |
Janet
Heasman |
| |
|
|
|
|
|