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The amphioxus genome illuminates vertebrate origins and cephalochordate biology

2008; Cold Spring Harbor Laboratory Press; Volume: 18; Issue: 7 Linguagem: Inglês

10.1101/gr.073676.107

1549-5469

Linda Z. Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito‐Gutiérrez, Matthew J. Blow, Marianne Bronner‐Fraser, Frédéric Brunet, Thomas Butts, Simona Candiani, Larry J. Dishaw, David Ferrier, Jordi García‐Fernàndez, Jeremy J. Gibson‐Brown, Carmela Gissi, Adam Godzik, Finn Hallböök, Dan Hirose, Kazuyoshi Hosomichi, Tetsuro Ikuta, Hidetoshi Inoko, Masanori Kasahara, Jun Kasamatsu, Takeshi Kawashima, Ayuko Kimura, Masaaki Kobayashi, Zbyněk Kozmík, Kaoru Kubokawa, Vincent Laudet, Gary W. Litman, Alice C. McHardy, Daniel Meulemans, Masaru Nonaka, Robert P. Olinski, Zeev Pancer, L Pennacchio, Mario Pestarino, Jonathan P. Rast, Isidore Rigoutsos, Marc Robinson‐Rechavi, Graeme J. Roch, Hidetoshi Saiga, Yasunori Sasakura, Masanobu Satake, Yutaka Satou, Michael Schubert, Nancy M. Sherwood, Takashi Shiina, Naohito Takatori, Javier A. Tello, Pavel Vopálenský, Shuichi Wada, Anlong Xu, Yuzhen Ye, Keita Yoshida, Fumiko Yoshizaki, J-R Yu, Qing Zhang, Christian M. Zmasek, Pieter J. de Jong, Kazutoyo Osoegawa, Nicholas H. Putnam, Daniel S. Rokhsar, Noriyuki Satoh, Peter W. H. Holland,

interferon and immune responses

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.