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De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin

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Abstract

Background

Blood clam (Anadara broughtonii) is a commercially important marine bivalve characterised by the red blood. Recently, the clams have been subjected to severe resource recession. Multiple environmental stressors are indispensable for the recession.

Objective

We aimed to investigate the transcriptome information of blood clam under environmental stressors.

Methods

Paired-end Illumina HiSeq™ 2500 sequencing technology was employed for cDNA library construction and Illumina sequencing. Several public databases were introduced for gene annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used for pathways analyses. The Open Reading Frame of annotated hemoglobin (Hb) was predicted and validated by DNAMAN 6.0 and NCBI BLASTx, respectively.

Results

A total of 242,919 transcripts were generated, 116,264 unigenes were subsequently assembled with an average length of 747 base pairs, and 33,776 unigenes were successfully annotated. Gene Ontology (GO) categories indicated that the terms of cellular processes, metabolic processes, cell, cell part, binding, and catalytic activity were dominant. KEGG pathway analyses suggested ribosome, oxytocin, focal adhesion, Ras, and PI3K-Akt were the largest signaling pathway groups, and many presented pathways (Ras, Rap1, and MAPK, etc.) were related to apoptosis, immune and stress response. In addition, a total of 19,306 potential simple sequence repeats (SSRs) were detected in 15,852 sequences. Six hemoglobin-related genes with complete conserved domain sequences were identified and 3 of them were predicted as HbI, HbIIα, and HbIIβ.

Conclusion

This study provides transcriptome responses to multiple environmental stressors in blood clams and would provide interesting hints for further studies.

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Acknowledgements

We would like to thank the staffs working in bivalve hatchery in Ling shanwei, Qingdao for providing experiment clams used in this study. This study was funded by the National Program on Key Basic Research Project (973 Program, 2015CB453302), and the Public Science and Technology Research Funds Projects of Ocean (201305043).

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Authors and Affiliations

  1. Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People’s Republic of China

    Yihang Wang, Shanshan Zhou, Tianyu Liu & Muyan Chen

  2. National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316004, People’s Republic of China

    Xiumei Zhang

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  1. Yihang Wang
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Contributions

ZX, and CM designed the study, WY prepared the manuscript, and reviewed it before submission. ZS and LT conducted the required experiments and performed data acquisition and analysis. All authors read and approved the final manuscript.

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Correspondence to Xiumei Zhang.

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Yihang Wang, Shanshan Zhou, Tianyu Liu, Muyan Chen, and Xiumei Zhang declare that they have no conflict of interest.

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Wang, Y., Zhou, S., Liu, T. et al. De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin. Genes Genom 42, 189–202 (2020). https://doi.org/10.1007/s13258-019-00887-7

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