@article{Holland01072008,
author = {Holland, Linda Z. and Albalat, Ricard and Azumi, Kaoru and Benito-Gutiérrez, Èlia and Blow, Matthew J. and Bronner-Fraser, Marianne and Brunet, Frederic and Butts, Thomas and Candiani, Simona and Dishaw, Larry J. and Ferrier, David E.K. and Garcia-Fernàndez, Jordi and Gibson-Brown, Jeremy J. and Gissi, Carmela and Godzik, Adam and Hallböök, Finn and Hirose, Dan and Hosomichi, Kazuyoshi and Ikuta, Tetsuro and Inoko, Hidetoshi and Kasahara, Masanori and Kasamatsu, Jun and Kawashima, Takeshi and Kimura, Ayuko and Kobayashi, Masaaki and Kozmik, Zbynek and Kubokawa, Kaoru and Laudet, Vincent and Litman, Gary W. and McHardy, Alice C. and Meulemans, Daniel and Nonaka, Masaru and Olinski, Robert P. and Pancer, Zeev and Pennacchio, Len A. and Pestarino, Mario and Rast, Jonathan P. and Rigoutsos, Isidore and Robinson-Rechavi, Marc and Roch, Graeme and Saiga, Hidetoshi and Sasakura, Yasunori and Satake, Masanobu and Satou, Yutaka and Schubert, Michael and Sherwood, Nancy and Shiina, Takashi and Takatori, Naohito and Tello, Javier and Vopalensky, Pavel and Wada, Shuichi and Xu, Anlong and Ye, Yuzhen and Yoshida, Keita and Yoshizaki, Fumiko and Yu, Jr-Kai and Zhang, Qing and Zmasek, Christian M. and de Jong, Pieter J. and Osoegawa, Kazutoyo and Putnam, Nicholas H. and Rokhsar, Daniel S. and Satoh, Noriyuki and Holland, Peter W.H.}, 
title = {The amphioxus genome illuminates vertebrate origins and cephalochordate biology},
volume = {18}, 
number = {7}, 
pages = {1100-1111}, 
year = {2008}, 
doi = {10.1101/gr.073676.107}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/18/7/1100.abstract}, 
eprint = {http://genome.cshlp.org/content/18/7/1100.full.pdf+html}, 
journal = {Genome Research} 
}