The transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A window into chordate evolution

Side view of living Asymmetron lucayanum
Publication TypeJournal Article
Year of Publication2014
AuthorsYue J.X, Yu J.K, Putnam N.H, Holland LZ
JournalGenome Biology and Evolution
Date Published2014/10
Type of ArticleArticle
ISBN Number1759-6653
Accession NumberWOS:000346775800009
KeywordsAmphioxus; Asymmetron; bayesian-estimation; Branchiostoma; central-nervous-system; chordate evolution; divergence times; dna-sequences; fossil calibrations; high-throughput; innate immunity; mitochondrial genome analysis; molecular clock; species; transcriptome; vertebrate origins

Cephalochordates, the sister group of tunicates plus vertebrates, have been called "living fossils" due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of similar to 120 Ma for A. lucayanum and B. floridae. The divisions between cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian.


"What our data underscore is the very slow rate of evolution of cephalochordates in general. Not surprisingly, modern cephalochordates are morphologically very much like the fossil cephalochordate from the mid-Cambrian, Pikaia, and, except for the absence of eyes and a smaller brain, very much like Haikouella, from the early Cambrian, which has been placed as the sister group of vertebrates (craniates) (Mallatt and Chen 2003). This low level of morphological evolution is congruent with the low rate of evolution at the genome level."

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