The amphioxus genome illuminates vertebrate origins and cephalochordate biology

TLDR

Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. The study aimed to enhance understanding of chordate evolution and vertebrate origins by extensively searching for genes, gene families, and conserved noncoding elements in the amphioxus genome. The authors performed an intensive genomic survey of Branchiostoma floridae, focusing on homeobox, opsin, neural crest, nuclear receptor, endocrine, immune genes, and conserved cis‑regulatory enhancers. The amphioxus genome contains a core set of chordate developmental and signaling genes—including a fifteenth Hox gene—many of which were later co‑opted in vertebrates for neural crest and adaptive immunity, and it preserves numerous conserved enhancers across vast phylogenetic distances while also exhibiting derived duplications of opsins and innate‑immunity genes, underscoring its value for understanding deuterostome and vertebrate evolution.

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.