The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.
Stein
Lincoln D
LD
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.. lstein@cshl.org
Bao
Zhirong
Z
Blasiar
Darin
D
Blumenthal
Thomas
T
Brent
Michael R
MR
Chen
Nansheng
N
Chinwalla
Asif
A
Clarke
Laura
L
Clee
Chris
C
Coghlan
Avril
A
Coulson
Alan
A
D'Eustachio
Peter
P
Fitch
David H A
DH
Fulton
Lucinda A
LA
Fulton
Robert E
RE
Griffiths-Jones
Sam
S
Harris
Todd W
TW
Hillier
LaDeana W
LW
Kamath
Ravi
R
Kuwabara
Patricia E
PE
Mardis
Elaine R
ER
Marra
Marco A
MA
Miner
Tracie L
TL
Minx
Patrick
P
Mullikin
James C
JC
Plumb
Robert W
RW
Rogers
Jane
J
Schein
Jacqueline E
JE
Sohrmann
Marc
M
Spieth
John
J
Stajich
Jason E
JE
Wei
C
C
Willey
David
D
Wilson
Richard K
RK
Durbin
Richard
R
Waterston
Robert H
RH
D000818:Animals; D005075:Biological Evolution; D002107:Caenorhabditis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D016000:Cluster Analysis; D003062:Codon; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005091:Exons; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods*; D020071:Interspersed Repetitive Sequences; D007438:Introns; D035683:MicroRNAs / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D005810:Multigene Family; D016366:Open Reading Frames; D020161:Physical Chromosome Mapping; D010957:Plasmids / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012335:RNA, Ribosomal / Q000235:genetics; D020038:RNA, Spliced Leader; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
D003062:Codon; D035683:MicroRNAs; D011506:Proteins; D012335:RNA, Ribosomal; D020038:RNA, Spliced Leader; D012313:RNA; D012343:RNA, Transfer