A comparative transcriptomic analysis in late embryogenesis of the red claw crayfish Cherax quadricarinatus

  • Yan Wang
  • Baojie Wang
  • Xuqing Shao
  • Mei Liu
  • Keyong Jiang
  • Mengqiang WangEmail author
  • Lei WangEmail author
Original Article


The red claw crayfish (Cherax quadricarinatus) is an emerging and important commercial species in several countries, and is also a potential biological model in crustacean biology. However, its molecular embryonic development mechanism remains largely unknown because of a lack of genomic resources and systematic research. A comprehensive and integrated transcriptomic analysis is necessary to reveal the cell biological function, gene expression profiles, and embryo patterning that occur during embryogenesis. In the present study, transcriptomic profiles of C. quadricarinatus embryos during three developmental stages were investigated by high-throughput Illumina sequencing technology, and the genes related to development were further analyzed. In total, 49,436 unigenes were assembled and clustered, in which 13,727 were annotated in the Nonredundant database, 5087 were classified based on Gene Ontology annotations, and 2735 were associated with 189 Kyoto Encyclopedia of Genes and Genomes pathways. Furthermore, gene expression differences among the embryos stages were analyzed, and 6658 differentially expressed genes (DEGs) were identified. In total, 3300, 5211, and 1262 DEGs were identified between the eye pigments forming stage (EP) and prepare-hatching stage (PH), EP and larvae (L), as well as PH and L; meanwhile, 1595, 2540 and 680 DEGs were annotated, respectively. The fundamental developmental genes related to apoptosis, neurogenesis, and segmentation, as well as signaling pathways related to Hedgehog, MAPK, Wnt, TGF-β and Notch, showed higher expression during the EP stage than in other two stages, indicating that the EP stage has more active biological processes than the latter stages. This transcriptome studies gene expression at different stages of embryonic development and the datasets provide a basis for understanding crustacean developmental biology and guiding seedling production.


Cherax quadricarinatus Embryonic development Transcriptome 



This work was supported by the National Natural Science Foundation of China (U1706209) and the Marine S&T Fund of Shandong Province for National Laboratory for Marine Science and Technology (2018SDKJ0502-2).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

438_2019_1621_MOESM1_ESM.jpg (176 kb)
Supplementary Fig. S1. The length distribution of unigenes. The X axis represents the different length intervals of unigenes. The Y axis represents the number of unigenes in each length interval. (JPEG 175 kb)
438_2019_1621_MOESM2_ESM.jpg (389 kb)
Supplementary Fig. S2. KEGG annotation of the total unigenes. (JPEG 388 kb)
438_2019_1621_MOESM3_ESM.jpg (163 kb)
Supplementary Fig. S3. Up- and downregulated genes of the EP, PH, and L stage embryos. (A) Comparison of upregulated genes. (B) Comparison of downregulated genes. (JPEG 162 kb)
438_2019_1621_MOESM4_ESM.jpg (8.7 mb)
Supplementary Fig. S4. GO classification of DEGs. (A) EP vs PH. (B) EP vs L. (C) PH vs L. (JPEG 8872 kb)
438_2019_1621_MOESM5_ESM.docx (20 kb)
Supplementary material 5 (DOCX 20 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.CAS Key Laboratory of Experimental Marine Biology, Institute of OceanologyChinese Academy of SciencesQingdaoChina
  2. 2.Laboratory for Marine Biology and BiotechnologyNational Laboratory for Marine Science and TechnologyQingdaoChina
  3. 3.University of Chinese Academy of SciencesBeijingChina
  4. 4.Research Platform for Marine Molecular Biotechnology, National Laboratory for Marine Science and TechnologyQingdaoChina
  5. 5.CAS Center for Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
  6. 6.Shandong Cigna Detection Technology Co., LtdQingdaoChina

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