A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations.

Authors

Che-Yi Lin, Wen-Hsin Hsu, Mei-Yeh Jade Lu, Yi-Hua Chen, Kun-Lung Li, Yi-Chih Chen, Yi-Hsien Su, Shen-Ju Chou, Jr-Kai Yu

Published in

Science advances. Volume 12. Issue 27. Pages eaee5076. Jul 03, 2026. Epub Jul 03, 2026.

Abstract

Comparative studies of vertebrate brains have elucidated the evolution of morphological diversity; yet, the fundamental chordate brain blueprint and the emergence of vertebrate-specific innovations remain elusive. To reconstruct the cellular and molecular origins of brain architecture in chordates, we combined single-nucleus RNA sequencing with spatial transcriptomics to generate a three-dimensional cell atlas of the central nervous system (CNS) in the early-branching chordate amphioxus. This atlas reveals a tripartite anterior-posterior organization comprising a rostral retinal/hypothalamic region, a di-mesencephalic domain, and a caudal hindbrain/spinal cord. Challenging previous views, we identify cell clusters resembling the vertebrate zona limitans intrathalamica and midbrain-hindbrain boundary regions that demarcate major brain compartments. Conversely, the absence of telencephalic marker expression in the amphioxus rostral forebrain suggests that the telencephalon is a vertebrate innovation. Collectively, our findings establish a spatial transcriptomic framework for the amphioxus CNS, providing crucial insight into the evolutionary origins of vertebrate brain complexity.

PMID:
42397914
Bibliographic data and abstract were imported from PubMed on 04 Jul 2026.

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