Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
Aparicio
Samuel
S
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609. saa1000@cam.ac.uk
Chapman
Jarrod
J
Stupka
Elia
E
Putnam
Nik
N
Chia
Jer-Ming
JM
Dehal
Paramvir
P
Christoffels
Alan
A
Rash
Sam
S
Hoon
Shawn
S
Smit
Arian
A
Gelpke
Maarten D Sollewijn
MD
Roach
Jared
J
Oh
Tania
T
Ho
Isaac Y
IY
Wong
Marie
M
Detter
Chris
C
Verhoef
Frans
F
Predki
Paul
P
Tay
Alice
A
Lucas
Susan
S
Richardson
Paul
P
Smith
Sarah F
SF
Clark
Melody S
MS
Edwards
Yvonne J K
YJ
Doggett
Norman
N
Zharkikh
Andrey
A
Tavtigian
Sean V
SV
Pruss
Dmitry
D
Barnstead
Mary
M
Evans
Cheryl
C
Baden
Holly
H
Powell
Justin
J
Glusman
Gustavo
G
Rowen
Lee
L
Hood
Leroy
L
Tan
Y H
YH
Elgar
Greg
G
Hawkins
Trevor
T
Venkatesh
Byrappa
B
Rokhsar
Daniel
D
Brenner
Sydney
S
D000818:Animals; D005075:Biological Evolution; D019295:Computational Biology; D017124:Conserved Sequence; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D005091:Exons; D029941:Fish Proteins / Q000737:chemistry / Q000235:genetics; D020440:Gene Duplication; D023061:Gene Order; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D007438:Introns; D020161:Physical Chromosome Mapping; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D020543:Proteome; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D026801:Synteny; D023741:Takifugu / Q000235:genetics*
D004251:DNA Transposable Elements; D029941:Fish Proteins; D011506:Proteins; D020543:Proteome