Transcript C. elegans was the first animal to have its genome (108 bp) completely sequenced. C.

C. elegans was the first animal to have its
genome (108 bp) completely sequenced.
C. elegans Genome in Numbers
Size
(Mb)
Protein
genes
Protein
genes/kb
95.53
19,141
4.98
Coding
Regions (%)
27
intergenic DNA
47%
exonic DNA
27%
intronic DNA
26%
% of genes
EST matches
(Mb)
38.9
The completed genome sequence is made up of
2,527 cosmids
113
fosmids
257
YACs
44
long range PCR products
http://nema.cap.ed.ac.uk/Caenorhabditis/C_elegans.html
Characteristics of the Caenorhabditis elegans genome
Seq
GenesEST’s
Inv. Rep.
Lev
Telom
Tand Rep
The C. elegans genome consortium, TIG 15:51, 1999
After
The
doing
study
“discovery
of many science”
aspects of
(L. Nematode
Hood, 2002;
“defining
biology
the
were
elements
made in
easier
biological
after objects”)
the genome
we
can of
do C.
regular
elegans
“hypothesis-driven”
was sequenced science.
Transplicing and operons in C. elegans
Outron
Blumenthal, T. (1998) - BioEssays 20:480-487.
Regulatory micro RNAs (miRNAs)
Involvement of small RNAs in the control of Temporal
development and RNAi in C. elegans
Banerjee & Slack BioEssays, 24:119, 2002
Feeding C. elegans with dsRNA turns off specific genes
Bacteria with no plasmid
24h
48h
72h
96h
Kamath e cols. (2001) Genome Biol. 2:1-10
Other nematodes help define what is
common to all species and what is
restricted to C. elegans at the molecular
level
SEM of CEW1 and C. elegans
CEW1
C. elegans
Anterior
Left side
Made by R. Turner Department of Biology, 1990 - Indiana University
Although the final morphology is the same, the induction
events during vulva development are difrerent in
C. elegans and CEW1
Dichtel et al., Genetics, 157:183, 2001
Transplicing in C. elegans and CEW1
CEW1
From Evans et al., PNAS 94:9751, 1997
Introns of the C. elegans vitellogenin genes
Winter, in: “Reproductive Biology of Invertebrates,Volume XII” - 2002
NJ-Tree of nematode vitellogenins (aminoacid sequences)
Winter, in: “Reproductive Biology of Invertebrates,Volume XII” - 2002
N- and C-terminus of nematode VTG evolve at
different rates
Winter et al., Mol. Biol. Evol., 13:674, 1996
Codon usage table of vit-6 genes in C. elegans and CEW1
Ce CEW1
Ce CEW1
Ce CEW1
CUU
51
24
CUC
39
55
CCC
CUA
1
2
1
CUG
0
12
CCA
99
64
CAA
9
CAG
Ce
85
17
15
83
GAU
50
23
GAC
50
77
CEW1
Winter et al., Mol. Biol. Evol., 13:674, 1996
Acknowledgements
Dr Cristiane Penha-Scarabotto
Dr Rubens Nobumoto Akamine
Joselene Pereira de Moura
Il-Young Ahn
Juliana Machado Andreoni
Paulo Afonso de Carvalho
Undergraduate
Daniela Peres Almenara
students
Manoel Aparecido Peres
SUPPORTED BY
&
“... We found that bringing together the true crossdisciplinary scientists was rendered difficult by the
fact that our academic center, and most academic
centers, live in a world of departments. And the
departments tend to create barriers both in how their
students are educated and what the expectations are
for faculty...” Leroy Hood, JAN/18/2002
[see http://www.oreillynet.com/pub/a/network/2002/01/18/hood.html]
http://www.oreillynet.com/biocon2002/?xA;
How are the genome sequences of C. elegans stored
Wormbase
Published in: http://nema.cap.ed.ac.uk/Caenorhabditis/C_elegans_genome/Celegansinformatics.html
MITE-like
Cele 42
Cele 1
Cele 2
Cele 14
Distribution of repetitive elements on the C. elegans chromosomes
Surzycki and William R. Belknap, PNAS 97:245–249, 2000
C. elegans behaviour is subjected to circadian variations
Osmotic
Shock Resistance
Movement
Saigusa et al., Curr. Biol. 12(2):R46, 2002
Kippert et al., Curr. Biol. 12(2):R47, 2002
Caenorhabditis elegans vitellogenin genes
gene
intron
nr.
location
DNA
strand
"YP"
Size of the
vitellogenin
(kDa)(*)
cDNA
clones
(**)
chromosome:
position
vit-1
4
K09F5.2
+
170B
186.6
17
X: 7,742,2017,746,243
vit-2
4
C42D8.2
+
170B
186.2
118
X: 5,114,3765,119,411
vit-3
5
F59D8.1
-
170A
185.0
1
X: 3,626,2243,612,142
vit-4
5
F59D8.2
-
170A
184.8
5
X: 3,618,0233,612,577
vit-5
5
C04F6.1
+
170A
184.9
69
X: 3,416,8333,421,907
vit-6
4
K07H8.6
+
115/
88
191.0
126
IV: 8,273,9688,279,162
* = calculated from the amino acid sequence deduced from the gene sequence; signal peptide excluded.
** = Number of cDNA clones listed in WormBase (http://www.wormbase.org/) (Jan/30/2001) associated with each gene
Winter, in: “Reproductive Biology of Invertebrates, Volume XII” - 2002
Embriogenesis of Acrobeloides nanus
Schierenberg (1999) - http://www.uni-koeln.de/math-nat-fak/zoologie/agschier/abschier3e.html
of man
Modified from: “Topics in Intern. Health – Schistosomiasis”
The Wellcome Trust