The amphioxus genome illuminates vertebrate origins and cephalochordate biology
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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.
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Similar expression patterns were observed in transgenic zebrafish bearing constructs for the orthologous human and pufferfish CNRs.
“Similar expression patterns were observed in transgenic zebra fi sh bearing constructs for the orthologous human and puffer fi sh CNRs (25, 26).”
From Transphyletic conservation of developmental regulatory state in animal evolution (2011) · cites this paper as [26]
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Self-citationŠestak, M. S., Božičević, V., Bakarić, R., Dunjko, V., & Domazet-Lošo, T. (2013) · Frontiers in Zoology · doi:10.1186/1742-9994-10-18 · Cited by 42 · see citing works
- Authors
- Holland, L. Z., Albalat, R., Azumi, K., Benito-Gutiérrez, È., Blow, M. J., Bronner-Fraser, M., Brunet, F., Butts, T., Candiani, S., Dishaw, L. J., Ferrier, D. E. K., Garcia-Fernàndez, J., Gibson-Brown, J. J., Gissi, C., Godzik, A., Hallböök, F., Hirose, D., Hosomichi, K., Ikuta, T., Inoko, H., Kasahara, M., Kasamatsu, J., Kawashima, T., Kimura, A., Kobayashi, M., Kozmik, Z., Kubokawa, K., Laudet, V., Litman, G. W., McHardy, A. C., Meulemans, D., Nonaka, M., Olinski, R. P., Pancer, Z., Pennacchio, L. A., Pestarino, M., Rast, J. P., Rigoutsos, I., Robinson-Rechavi, M., Roch, G., Saiga, H., Sasakura, Y., Satake, M., Satou, Y., Schubert, M., Sherwood, N., Shiina, T., Takatori, N., Tello, J., Vopalensky, P., Wada, S., Xu, A., Ye, Y., Yoshida, K., Yoshizaki, F., Yu, J.-K., Zhang, Q., Zmasek, C. M., de Jong, P. J., Osoegawa, K., Putnam, N. H., Rokhsar, D. S., Satoh, N., & Holland, P. W. H.
- Affiliations
- Scripps Institution of Oceanography (US)
- Universitat de Barcelona (ES)
- Hokkaido University (JP)
- Joint Genome Institute (US)
- California Institute of Technology (US)
- University of Oxford (GB)
- University of Genoa (IT)
- Moffitt Cancer Center (US)
- University of St Andrews (GB)
- University of Milan (IT)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- Uppsala University (SE)
- Tokyo Metropolitan University (JP)
- Tokai University (JP)
- University of California, Berkeley (US)
- The University of Tokyo (JP)
- Lyon 1 Université (FR)
- IBM Research - Thomas J. Watson Research Center (US)
- University of Maryland, Baltimore (US)
- University of Toronto (CA)
- University of Victoria (CA)
- University of Tsukuba (JP)
- Tohoku University (JP)
- Kyoto University (JP)
- Nagahama Institute of Bio-Science and Technology (JP)
- Sun Yat-sen University (CN)
- Juntendo University (JP)
- ORCID
- Holland, Linda Z.
- Albalat, Ricard
- Blow, Matthew J.
- Bronner-Fraser, Marianne
- Butts, Thomas
- Candiani, Simona
- Dishaw, Larry J.
- Ferrier, David E.K.
- Gissi, Carmela
- Godzik, Adam
- Hallböök, Finn
- Hosomichi, Kazuyoshi
- Ikuta, Tetsuro
- Kasahara, Masanori
- Kasamatsu, Jun
- Kawashima, Takeshi
- Kimura, Ayuko
- Kobayashi, Masaaki
- Laudet, Vincent
- McHardy, Alice C.
- Pennacchio, Len A.
- Pestarino, Mario
- Rast, Jonathan P.
- Rigoutsos, Isidore
- Saiga, Hidetoshi
- Sasakura, Yasunori
- Satou, Yutaka
- Schubert, Michael
- Shiina, Takashi
- Tello, Javier
- Xu, Anlong
- Ye, Yuzhen
- Yoshida, Keita
- Zmasek, Christian M.
- Osoegawa, Kazutoyo
- Putnam, Nicholas H.
- Rokhsar, Daniel S.
- Satoh, Noriyuki
- Holland, Peter W.H.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-06-18
- Volume
- 18
- Issue
- 7
- Pages
- 1100-1111
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2493399
- OpenAlex
- W2135740919
- Cited by
- 512
- References
- 86
- Citations by year
- 2026: 4 · 2025: 14 · 2024: 10 · 2023: 8 · 2022: 14 · 2021: 12 · 2020: 23 · 2019: 13 · 2018: 23 · 2017: 21 · 2016: 23 · 2015: 32 · 2014: 41 · 2013: 42 · 2012: 55
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by-nc)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
- HAL (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- CINECA IRIS Institutial Research Information System (University of Genoa) (submittedVersion)
- IRIS (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Sunderland Repository (University of Sunderland) (submittedVersion)
- Funders
- National Science Foundation
- Wellcome Trust
- European Commission
- Ministry of Education, Culture, Sports, Science and Technology
- Ministero dell’Istruzione, dell’Università e della Ricerca (FIRB_2001)
- Centre National de la Recherche Scientifique
- National Institutes of Health
- Biotechnology and Biological Sciences Research Council (BBS/B/12067/2, BBS/B/12067)
- Japan Society for the Promotion of Science
- National Institute of Allergy and Infectious Diseases (R01AI023338)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- amphioxus, Branchiostoma floridae, cephalochordates, vertebrate origin, chordate evolution, Hox genes, homeobox genes, opsin genes, neural crest development, nuclear receptors, cis-regulatory enhancers, whole-genome duplication, paralogs, adaptive immunity, innate immunity, endocrine system, tunicates, gene loss
- MeSH terms
- Animals, Chordata, Nonvertebrate, Genes, Homeobox, Humans, Mice, Transgenic, Phylogeny, Vertebrates, Genome, Evolution, Molecular, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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