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