RT Journal
A1 Holland, Linda Z.
A1 Albalat, Ricard
A1 Azumi, Kaoru
A1 Benito-Gutiérrez, Èlia
A1 Blow, Matthew J.
A1 Bronner-Fraser, Marianne
A1 Brunet, Frederic
A1 Butts, Thomas
A1 Candiani, Simona
A1 Dishaw, Larry J.
A1 Ferrier, David E.K.
A1 Garcia-Fernàndez, Jordi
A1 Gibson-Brown, Jeremy J.
A1 Gissi, Carmela
A1 Godzik, Adam
A1 Hallböök, Finn
A1 Hirose, Dan
A1 Hosomichi, Kazuyoshi
A1 Ikuta, Tetsuro
A1 Inoko, Hidetoshi
A1 Kasahara, Masanori
A1 Kasamatsu, Jun
A1 Kawashima, Takeshi
A1 Kimura, Ayuko
A1 Kobayashi, Masaaki
A1 Kozmik, Zbynek
A1 Kubokawa, Kaoru
A1 Laudet, Vincent
A1 Litman, Gary W.
A1 McHardy, Alice C.
A1 Meulemans, Daniel
A1 Nonaka, Masaru
A1 Olinski, Robert P.
A1 Pancer, Zeev
A1 Pennacchio, Len A.
A1 Pestarino, Mario
A1 Rast, Jonathan P.
A1 Rigoutsos, Isidore
A1 Robinson-Rechavi, Marc
A1 Roch, Graeme
A1 Saiga, Hidetoshi
A1 Sasakura, Yasunori
A1 Satake, Masanobu
A1 Satou, Yutaka
A1 Schubert, Michael
A1 Sherwood, Nancy
A1 Shiina, Takashi
A1 Takatori, Naohito
A1 Tello, Javier
A1 Vopalensky, Pavel
A1 Wada, Shuichi
A1 Xu, Anlong
A1 Ye, Yuzhen
A1 Yoshida, Keita
A1 Yoshizaki, Fumiko
A1 Yu, Jr-Kai
A1 Zhang, Qing
A1 Zmasek, Christian M.
A1 de Jong, Pieter J.
A1 Osoegawa, Kazutoyo
A1 Putnam, Nicholas H.
A1 Rokhsar, Daniel S.
A1 Satoh, Noriyuki
A1 Holland, Peter W.H.
T1 The amphioxus genome illuminates vertebrate origins and cephalochordate biology
JF Genome Research 
JO Genome Research 
YR 2008 
FD July 01 
VO 18 
IS 7 
SP 1100 
OP 1111 
DO 10.1101/gr.073676.107 
UL http://genome.cshlp.org/content/18/7/1100.abstract 
AB 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.