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De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress

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Abstract

Rising seawater temperatures cause coral bleaching. The molecular responses of the coral holobiont under stress conditions, determine the success of the symbiosis. Anomastraea irregularis is a hard coral commonly found in the harsh intertidal zones of the south coast of KwaZulu-Natal (KZN), South Africa, where it thrives at the very margins of hard coral distribution in the Western Indian Ocean. To identify the possible molecular and cellular mechanisms underlying its resilience to heat stress, experimental and control nubbins were exposed to temperatures of 29 and 19 °C respectively for 24 h. The transcriptome was assembled de novo from 42.8 million quality controlled 63 bp paired-end short sequence reads obtained via RNA sequencing (RNA-seq). The assembly yielded 333,057 contigs (> 500 bp = 55,626, Largest = 6341 bp N50 = 747 bp). 1362 (1.23%) of the transcripts were significantly differentially expressed between heat stressed and control samples. Log fold change magnitudes among individual genes ranged from − 4.6 to 7.2. Overall, the heat stress response in the A. irregularis constituted a protective response involving up regulation of apoptosis and SUMOylation. Gene ontology (GO) analyses revealed that heat stress in the coral affected the metabolism, protein synthesis, photosynthesis, transport and cytoskeleton. This is the first study to produce a reference transcriptome of this coral species and analyze its response to heat stress. The assembled transcriptome also presents a valuable resource for further transcriptomic and genomic studies.

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The transcriptome data will be uploaded to Springer Nature Research Data Support.

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Acknowledgements

We thank postgraduate students in the Marine Biology and Marine Evolution Laboratories for their invaluable support during sampling and nucleic acid extractions. Special thanks go to Centre for Proteomic and Genomic Research (CPGR) South Africa for sequencing services. We appreciate the assistance from the technical and administrative staff in the school of Life sciences, University of KwaZulu-Natal, Westville Campus.

Funding

This research was supported by the National Research Fund (NRF) South Africa, and Gay Langmuir Bursary.

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Authors and Affiliations

  1. School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa

    Christine A. Onyango, David Glassom & Angus MacDonald

  2. School of Natural Sciences, Masinde Muliro University of Science and Technology, Kakamega, 50100, Kenya

    Christine A. Onyango

Authors
  1. Christine A. Onyango
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  2. David Glassom
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by CAO. The first draft of the manuscript was written by CAO, and all authors commented on previous versions of the paper. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Christine A. Onyango.

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Conflict of interest

On behalf of the authors, the corresponding author states that there is no conflict of interest.

Ethical approval

No ethics approval was required as the coral is not considered endangered. Sampling permit number RES 2019/93 was used.

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Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file 1 (DOCX 14 KB) Online Resource 1 Table showing total RNA quality and quantity

11033_2021_6184_MOESM2_ESM.docx

Supplementary file 2 (DOCX 14 KB) Online Resource 2 Quast generated statistics of the assembled A. irregularis transcriptome

Supplementary file 3 (FASTA 149 MB) Online Resource 3 De novo assembled A. irregularis transcriptome.

Supplementary file 4 (XLSX 153 KB) Online Resource 4 List of significantly differentially expressed transcripts

11033_2021_6184_MOESM5_ESM.jpg

Supplementary file 5 (JPG 195 KB) Online Resource 5 MA plot showing log fold changes of differentially expressed genes between A. irregularis heat stressed and control samples. Each of the dots represent transcripts. Significantly differentially expressed transcripts are coloured in red

Supplementary file 6 (FASTA 16.1 MB) Online Resource 6 Coding sequences from A. irregularis heat stressed samples.

Supplementary file 7 (FASTA 21.1 MB) Online Resource 7 Coding sequences from A. irregularis control samples

11033_2021_6184_MOESM8_ESM.docx

Supplementary file 8 (DOCX 14 KB) Online Resource 8 Quast generated de novo transcriptome post-processing metrics (processing of de novo assembled transcripts into putative coding sequences)

11033_2021_6184_MOESM9_ESM.png

Supplementary file 9 (PNG 291 KB) Online Resource 9 Annotation distribution among (A) A. irregularis heat stressed (B) A. irregularis control contigs

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Onyango, C.A., Glassom, D. & MacDonald, A. De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress. Mol Biol Rep 48, 2083–2092 (2021). https://doi.org/10.1007/s11033-021-06184-5

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