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Development of a high-resolution molecular marker for tracking Pseudo-nitzschia pungens genetic diversity through comparative analysis of mitochondrial genomes

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Abstract

The harmful algal bloom (HAB) species Pseudo-nitzschia pungens is widely distributed in almost all continents. Accumulating evidence suggests that P. pungens has high genetic diversity and many strains can produce the toxin domoic acid (DA) that harms animals and humans. Nevertheless, different P. pungens strains cannot be distinguished using morphological features or using common molecular markers including 18S rDNA, 28S rDNA, ITS, cox1, and rbcL. As such, high-resolution molecular markers need to be developed to resolve P. pungens genetic diversity, facilitating accurate tracking of toxic P. pungens strains. We hypothesized that molecular markers with high resolution and high specificity can be designed through identifying regions with high genomic variations in the mitochondrial genome. Here, we describe the development of a new molecular marker Pseudo-nitzschia pungens mitochondrial 1 (ppmt1) with high resolution and high specificity through comparative analysis of mitochondrial genomes of nine P. pungens strains isolated from coastal regions of China. In conclusion, we have developed ppmt1 as a high-resolution and high-specificity molecular marker for tracking strains and genetic diversity of the HAB species P. pungens.

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Acknowledgements

We are grateful to colleagues from the Jiaozhou Bay Marine Ecosystem Research Station for their help in field sampling. The samples from the Bohai Sea were supported by the National Natural Science Foundation of China, Bohai and Yellow Sea Oceanography Expedition (NORC2019-01). Data acquisition and sample collections from the East China Sea were supported by National Natural Science Foundation of China (NSFC) Open Research Cruise (Cruise No. NORC2019-2), funded by Shiptime Sharing Project of NSFC. This cruise was conducted onboard R/V “Xiang Yang Hong 18” by The First Institute of Oceanography, Ministry of Natural Resources, China.

Funding

This research was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDB42000000), Chinese Academy of Sciences Pioneer Hundred Talents Program (to Nansheng Chen), Taishan Scholar Project Special Fund (to Nansheng Chen), Qingdao Innovation and Creation Plan (Talent Development Program-5th Annual Pioneer and Innovator Leadership Award to Nansheng Chen, 19-3-2-16-zhc), the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (No. QYZDB-SSW-DQC023) (to Feng Liu), and the Major Scientific and Technological Innovation Project of Shandong Province (No. 2019JZZY020706) (to Feng Liu).

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  1. CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Yang Chen, Yichao Wang, Kuiyan Liu, Feng Liu & Nansheng Chen

  2. Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China

    Yang Chen, Yichao Wang, Kuiyan Liu, Feng Liu & Nansheng Chen

  3. University of Chinese Academy of Sciences, Beijing, 10039, China

    Yang Chen, Yichao Wang & Kuiyan Liu

  4. Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China

    Yang Chen, Yichao Wang, Kuiyan Liu, Feng Liu & Nansheng Chen

  5. Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada

    Nansheng Chen

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Fig. S1

The collection sites of nine Pseudo-nitzschia pungens strains. In the Bohai Sea, five strains (CNS00110 and CNS00153 - CNS00156) were isolated from site A, and strain CNS00141 was isolated from site B. Strain CNS00055 was isolated from site C in the Jiaozhou Bay. In the East China Sea, strain CNS00089 was isolated from site D and strain CNS00043 was isolated from site E (PDF 1453 kb)

Fig. S2

Phylogenetic trees based on maximum likelihood (ML) analysis of five common markers 18S rDNA, 28S rDNA D1-3 domain, cox1, and rbcL. (a) ML phylogenetic tree based on the marker 18S rDNA; (b) ML phylogenetic tree based on the marker 28S rDNA D1-3 domain; (c) ML phylogenetic tree based on the marker cox1 partial sequence; (d) ML phylogenetic tree based on the marker rbcL (PDF 398 kb)

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Chen, Y., Wang, Y., Liu, K. et al. Development of a high-resolution molecular marker for tracking Pseudo-nitzschia pungens genetic diversity through comparative analysis of mitochondrial genomes. J Appl Phycol 33, 2283–2298 (2021). https://doi.org/10.1007/s10811-021-02461-9

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