The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution

Yue, Jia-Xing; Yu, Jr-Kai; Putnam, Nicholas H.; Holland, Linda Z.

doi:10.1093/gbe/evu212

The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution

Journal Article · Fri Sep 19 00:00:00 EDT 2014 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evu212· OSTI ID:1625337

Yue, Jia-Xing ^[1]; Yu, Jr-Kai ^[2]; Putnam, Nicholas H. ^[3]; Holland, Linda Z. ^[4]

Rice Univ., Houston, TX (United States). BioSciences; DOE/OSTI
Academia Sinica, Taipei (Taiwan). Inst. of Cellular and Organismic Biology
Rice Univ., Houston, TX (United States). BioSciences
Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography. Marine Biology Research Division

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 ~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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625337

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 10 Vol. 6; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development Yang, Kevin Yi; Chen, Yuan; Zhang, Zuming Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep23195	journal	March 2016
The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus) Yue, Jia-Xing; Holland, Nicholas D.; Holland, Linda Z. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep28350	journal	June 2016
Putative extremely high rate of proteome innovation in lancelets might be explained by high rate of gene prediction errors Bányai, László; Patthy, László Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30700	journal	August 2016
Genome-wide gene expression analysis of amphioxus ( Branchiostoma belcheri ) following lipopolysaccharide challenge using strand-specific RNA-seq Zhang, Qi-Lin; Zhu, Qian-Hua; Xie, Zheng-Qing RNA Biology, Vol. 14, Issue 12 https://doi.org/10.1080/15476286.2017.1367890	journal	September 2017
Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle Yue, Jia-Xing; Kozmikova, Iryna; Ono, Hiroki Genome Biology and Evolution, Vol. 8, Issue 8 https://doi.org/10.1093/gbe/evw158	journal	July 2016
Whole-Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand-New Variant Dataset for Branchiostoma Bi, Changwei; Lu, Na; Han, Tingyu BioMed Research International, Vol. 2020 https://doi.org/10.1155/2020/3697342	journal	January 2020
In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus) Wang, Le; Yu, Cuiping; Guo, Liang PLOS ONE, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pone.0145868	journal	December 2015
Genome-wide comparison of the protein-coding repertoire reveals fast evolution of immune-related genes in cephalochordates and Osteichthyes superclass Zhang, Qi-Lin; Xu, Bin; Wang, Xiu-Qiang Oncotarget, Vol. 9, Issue 1 https://doi.org/10.18632/oncotarget.22749	journal	November 2017
A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus Zhang, Qi-Lin; Zhang, Guan-Ling; Yuan, Ming-Long Frontiers in Physiology, Vol. 9 https://doi.org/10.3389/fphys.2018.01833	journal	December 2018
Morphological Stasis and Proteome Innovation in Cephalochordates Bányai, László; Kerekes, Krisztina; Trexler, Mária Genes, Vol. 9, Issue 7 https://doi.org/10.3390/genes9070353	journal	July 2018
Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors Furlong, Michael; Seong, Jae Young Biomolecules & Therapeutics, Vol. 25, Issue 1 https://doi.org/10.4062/biomolther.2016.199	journal	January 2017
Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus Zieger, Elisabeth; Garbarino, Greta; Robert, Nicolas S. M. Cellular and Molecular Life Sciences, Vol. 75, Issue 13 https://doi.org/10.1007/s00018-017-2734-3	journal	January 2018
Prevertebrate Local Gene Duplication Facilitated Expansion of the Neuropeptide GPCR Superfamily Yun, Seongsik; Furlong, Michael; Sim, Mikang Molecular Biology and Evolution, Vol. 32, Issue 11 https://doi.org/10.1093/molbev/msv179	journal	September 2015
The origin and evolution of chordate nervous systems Holland, Linda Z. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1684 https://doi.org/10.1098/rstb.2015.0048	journal	December 2015
Wnt evolution and function shuffling in liberal and conservative chordate genomes Somorjai, Ildikó M. L.; Martí-Solans, Josep; Diaz-Gracia, Miriam Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1468-3	journal	July 2018

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