The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA. lzholland@ucsd.edu
Linda Z
LZ
Holland
Ricard
R
Albalat
Kaoru
K
Azumi
Elia
E
Benito-Gutiérrez
Matthew J
MJ
Blow
Marianne
M
Bronner-Fraser
Frederic
F
Brunet
Thomas
T
Butts
Simona
S
Candiani
Larry J
LJ
Dishaw
David E K
DE
Ferrier
Jordi
J
Garcia-Fernàndez
Jeremy J
JJ
Gibson-Brown
Carmela
C
Gissi
Adam
A
Godzik
Finn
F
Hallböök
Dan
D
Hirose
Kazuyoshi
K
Hosomichi
Tetsuro
T
Ikuta
Hidetoshi
H
Inoko
Masanori
M
Kasahara
Jun
J
Kasamatsu
Takeshi
T
Kawashima
Ayuko
A
Kimura
Masaaki
M
Kobayashi
Zbynek
Z
Kozmik
Kaoru
K
Kubokawa
Vincent
V
Laudet
Gary W
GW
Litman
Alice C
AC
McHardy
Daniel
D
Meulemans
Masaru
M
Nonaka
Robert P
RP
Olinski
Zeev
Z
Pancer
Len A
LA
Pennacchio
Mario
M
Pestarino
Jonathan P
JP
Rast
Isidore
I
Rigoutsos
Marc
M
Robinson-Rechavi
Graeme
G
Roch
Hidetoshi
H
Saiga
Yasunori
Y
Sasakura
Masanobu
M
Satake
Yutaka
Y
Satou
Michael
M
Schubert
Nancy
N
Sherwood
Takashi
T
Shiina
Naohito
N
Takatori
Javier
J
Tello
Pavel
P
Vopalensky
Shuichi
S
Wada
Anlong
A
Xu
Yuzhen
Y
Ye
Keita
K
Yoshida
Fumiko
F
Yoshizaki
Jr-Kai
JK
Yu
Qing
Q
Zhang
Christian M
CM
Zmasek
Pieter J
PJ
de Jong
Kazutoyo
K
Osoegawa
Nicholas H
NH
Putnam
Daniel S
DS
Rokhsar
Noriyuki
N
Satoh
Peter W H
PW
Holland
D000818:Animals; D002816:Chordata, Nonvertebrate / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D005801:Genes, Homeobox; D016678:Genome; D006801:Humans; D051379:Mice; D008822:Mice, Transgenic; D010802:Phylogeny; D014714:Vertebrates / Q000235:genetics* / Q000502:physiology