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

C. elegans Genome in Numbers

Size(Mb)

Proteingenes

Protein genes/

kb

CodingRegions (%)

% of genes EST

matches(Mb)

95.53 19,141

4.98 27 38.9

The completed genome sequence is made up of

2,527 cosmids

113 fosmids

257 YACs

44 long range PCR products

intergenic DNA 47%

exonic DNA 27%

intronic DNA 26%

http://nema.cap.ed.ac.uk/Caenorhabditis/C_elegans.html

Characteristics of the Caenorhabditis elegans genomeSeq

GenesEST’sLev

Inv. Rep.

Tand RepTelom

The C. elegans genome consortium, TIG 15:51, 1999

The study of many aspects of Nematode biology were made easier after the genome of C. elegans was sequenced

After doing “discovery science” (L. Hood, 2002; “defining the elements in biological objects”) we can do regular “hypothesis-driven” science.

Outron

Transplicing and operons in C. elegans

Blumenthal, T. (1998) - BioEssays 20:480-487.

Regulatory micro RNAs (miRNAs)

Banerjee & Slack BioEssays, 24:119, 2002

Involvement of small RNAs in the control of Temporal development and RNAi in C. elegans

24h

48h

72h

96h

Bacteria with no plasmid

Kamath e cols. (2001) Genome Biol. 2:1-10

Feeding C. elegans with dsRNA turns off specific genes

Other nematodes help define what is common to all species and what is restricted to C. elegans at the molecular level

Made by R. Turner Department of Biology, 1990 - Indiana University

CEW1 C. elegans

Anterior

Left side

SEM of CEW1 and C. elegans

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

CEW1

Transplicing in C. elegans and 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

CUU

CUC

CUA

CUG

51 24

39 55

1 2

0 12CCA

CCC 1

99

64

985 17

15 83

CAA

CAG

GAU

GAC

50

50

23

77

Ce CEW1 CEW1Ce Ce CEW1 Ce CEW1

Codon usage table of vit-6 genes in C. elegans and CEW1

Winter et al., Mol. Biol. Evol., 13:674, 1996

Acknowledgements

Dr Cristiane Penha-Scarabotto

Dr Rubens Nobumoto AkamineJoselene Pereira de MouraIl-Young Ahn

Juliana Machado AndreoniPaulo Afonso de Carvalho

Daniela Peres Almenara

Manoel Aparecido Peres

SUPPORTED BY &

Undergraduatestudents

“... We found that bringing together the true cross-disciplinary 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;

Wormbase

How are the genome sequences of C. elegans stored

Published in: http://nema.cap.ed.ac.uk/Caenorhabditis/C_elegans_genome/Celegansinformatics.html

Distribution of repetitive elements on the C. elegans chromosomes

Surzycki and William R. Belknap, PNAS 97:245–249, 2000

Cel

e 14

Cel

e 2

Cel

e 1

MIT

E-li

keC

ele

42

Saigusa et al., Curr. Biol. 12(2):R46, 2002

Movement

Kippert et al., Curr. Biol. 12(2):R47, 2002

Osmotic Shock Resistance

C. elegans behaviour is subjected to circadian variations

Caenorhabditis elegans vitellogenin genes

gene intron nr.

location

DNA stran

d

"YP"

Size of the

vitellogenin (kDa)

(*)

cDNA clones

(**)

chromosome: position

vit-1 4 K09F5.2

+ 170B

186.6 17 X: 7,742,201-7,746,243

vit-2 4 C42D8.2

+ 170B

186.2 118 X: 5,114,376-5,119,411

vit-3 5 F59D8.1

- 170A

185.0 1 X: 3,626,224-3,612,142

vit-4 5 F59D8.2

- 170A

184.8 5 X: 3,618,023-3,612,577

vit-5 5 C04F6.1

+ 170A

184.9 69 X: 3,416,833-3,421,907

vit-6 4 K07H8.6

+ 115/88

191.0 126 IV: 8,273,968-8,279,162

* = 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