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Open Access Research article

Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine

Zhengyuan Wang123, Jianguo Du45, Siew Hong Lam2, Sinnakarupan Mathavan6, Paul Matsudaira123* and Zhiyuan Gong12*

Author Affiliations

1 Computation and Systems Biology, Singapore-MIT Alliance, 117543, Singapore

2 Department of Biological Sciences, National University of Singapore, 117543, Singapore

3 NUS Centre for BioImaging Sciences, National University of Singapore, 117543, Singapore

4 Dept of Oceanography, Xiamen University, Xiamen, 361005, China

5 Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China

6 Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore

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BMC Genomics 2010, 11:392  doi:10.1186/1471-2164-11-392

Published: 22 June 2010



The zebrafish intestine is a simple tapered tube that is folded into three sections. However, whether the intestine is functionally similar along its length remains unknown. Thus, a systematic structural and functional characterization of the zebrafish intestine is desirable for future studies of the digestive tract and the intestinal biology and development.


To characterize the structure and function of the adult zebrafish intestine, we divided the intestine into seven roughly equal-length segments, S1-S7, and systematically examined the morphology of the mucosal lining, histology of the epithelium, and molecular signatures from transcriptome analysis. Prominent morphological features are circumferentially-oriented villar ridges in segments S1-S6 and the absence of crypts. Molecular characterization of the transcriptome from each segment shows that segments S1-S5 are very similar while S6 and S7 unique. Gene ontology analyses reveal that S1-S5 express genes whose functions involve metabolism of carbohydrates, transport of lipids and energy generation, while the last two segments display relatively limited function. Based on comparative Gene Set Enrichment Analysis, the first five segments share strong similarity with human and mouse small intestine while S6 shows similarity with human cecum and rectum, and S7 with human rectum. The intestinal tract does not display the anatomical, morphological, and molecular signatures of a stomach and thus we conclude that this organ is absent from the zebrafish digestive system.


Our genome-wide gene expression data indicate that, despite the lack of crypts, the rostral, mid, and caudal portions of the zebrafish intestine have distinct functions analogous to the mammalian small and large intestine, respectively. Organization of ridge structures represents a unique feature of zebrafish intestine, though they produce similar cross sections to mammalian intestines. Evolutionary lack of stomach, crypts, Paneth cells and submucosal glands has shaped the zebrafish intestine into a simpler but unique organ in vertebrate intestinal biology.