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Full-length transcriptome sequencing and comparative transcriptomic analysis of different developmental stages of the sporophyll in Undaria pinnatifida (Laminariales: Alariaceae)

Journal of Applied Phycology volume 32, pages 2081–2092 (2020)Cite this article

Abstract

Sporophyll development is an important biological process which is crucial to reproduction of the sporophyte of the brown alga Undaria pinnatifida. However, the molecular foundation underlying this process is largely unknown due to lack of genomic information in this important alga. Full-length transcriptome, which covered male and female gametophytes at vegetative and gametogenic phases, and the blade, stipe, immature and mature parts of the sporophyll of sporophytes, was obtained for the first time through single molecule real-time sequencing in this study. After removing potentially polluted sequences derived from microorganisms, we obtained a total of 61,181 transcripts with average and N50 length being 1639 and 1815 bp, respectively, and annotated 21,915 of them (35.8%). By using the full-length transcriptome as reference, we performed Illumina sequencing to analyze the difference of gene expression among different developmental stages of the sporophyll and validated the results by quantitative real-time PCR. A large number of transcripts related to flagellar components and fucoidan biosynthesis as well as a few transcripts coding for meiotic nuclear division protein were found to be significantly upregulated with development of the sporophyll, and thus the over-expression of them is likely essential for the sporophyll to perform its biological function. These findings contribute to our understanding of sporophyll development in U. pinnatifida at the transcriptional level.

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Acknowledgments

We would like to thank Suqin Gao and Cuimei Zhang for their help in culturing the sporophytes in laboratory.

Funding

This research was funded by the National Natural Science Foundation of China (No. 41676128), Biological Resources Program from Chinese Academy of Sciences (KFJ-BRP-017-27), China Agriculture Research System (CARS-50), the Taishan Scholar Program of Shandong Province, and the Foundation for Huiquan Scholar of Institute of Oceanology, Chinese Academy of Sciences.

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Authors and Affiliations

  1. CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China

    Tifeng Shan, Qianxi Li, Xuemei Wang & Shaojun Pang

  2. Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China

    Tifeng Shan, Qianxi Li, Xuemei Wang & Shaojun Pang

  3. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd., Qingdao, 266071, China

    Tifeng Shan, Qianxi Li, Xuemei Wang & Shaojun Pang

  4. University of Chinese Academy of Sciences, Beijing, 100049, China

    Qianxi Li & Xuemei Wang

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  1. Tifeng Shan
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  2. Qianxi Li
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  3. Xuemei Wang
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  4. Shaojun Pang
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Contributions

TFS and SJP designed the entire study and wrote the manuscript. TFS cultured the gametophytes and sporophytes. TFS, QXL, and XMW extracted RNA, performed the qRT-PCR, and analyzed the data. All authors read and approved the final manuscript.

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Correspondence to Tifeng Shan or Shaojun Pang.

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Fig. S1

Top 10 species showing homology to the full-length transcriptome of Undaria pinnatifida in nonredundant protein (Nr) databases. (PDF 122 kb).

Fig. S2

Annotation of the full-length transcriptome of Undaria pinnatifida in database of euKaryotic Ortholog Groups (KOG). (PDF 151 kb).

Fig. S3

Pearson’s correlation between different biological replicates. (PDF 7 kb).

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Shan, T., Li, Q., Wang, X. et al. Full-length transcriptome sequencing and comparative transcriptomic analysis of different developmental stages of the sporophyll in Undaria pinnatifida (Laminariales: Alariaceae). J Appl Phycol 32, 2081–2092 (2020). https://doi.org/10.1007/s10811-020-02080-w

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  • DOI: https://doi.org/10.1007/s10811-020-02080-w

Keywords

  • Phaeophyceae
  • SMRT sequencing
  • Sporophyll development
  • Flagellum
  • Fucoidan
  • Meiotic nuclear division