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Published June 18, 2008 | Supplemental Material + Published
Journal Article Open

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

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.

Additional Information

© 2008 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Article published online before print. Received October 26, 2007; accepted in revised form February 24, 2008. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.073676.107 This work was funded by grants from the National Science Foundation, USA (L.Z.H.), National Institutes of Health, USA (G.W.L.), the Wellcome Trust (P.W.H.H.), BBSRC, UK (D.E.K.F., T.B., P.W.H.H.), and MEXT, Japan (H.S., N.S.), Center for Applied Genomics MSMT and Academy of Sciences, Czech Republic (Z.K.), and the 21st Century and Global COEs at Kyoto University (N. S.), from Ministerio de Educación y Ciencia, Spain (J.G.-F.), MIUR Italy, FIRB 2001 BAU01WAFY (S.C., M.P.), JSPS, Japan (H.S.), and JSPS, Japan, CNRS and CRESCENDO, a European Union Integrated Project of FP6 (V.L., M.S.).

Attached Files

Published - 1100.full.pdf

Supplemental Material - Holland_Supplemental_references.doc

Supplemental Material - Holland_supplemental_figures-revised.pdf

Supplemental Material - Holland_supplemental_methods.doc

Supplemental Material - Holland_supplemental_tables-revised.pdf

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Additional details

Created:
August 19, 2023
Modified:
October 17, 2023