Acta Oceanologica Sinica

, Volume 37, Issue 4, pp 89–101 | Cite as

Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae

  • Shanshan Wang
  • Lei Zhang
  • Shan Chi
  • Guoliang Wang
  • Xumin Wang
  • Tao Liu
  • Xuexi Tang


Carotenoids play a crucial role in absorbing light energy for photosynthesis, as well as in protecting chlorophyll from photodamage. In contrast to the Streptophyta, few studies have examined carotenoid biosynthetic pathways in algae, owing to a shortage of datasets. As part of the 1000 Plants Project, we sequenced and assembled the transcriptomes of 41 marine macroalgal species, including 22 rhodophytes and 19 phaeophytes, and then combined the datasets with publicly available data from GenBank (National Center for Biotechnology Information) and the U.S. Department of Energy Joint Genome Institute. As a result, we identified 68 and 79 fulllength homologs in the Rhodophyta and Phaeophyceae, respectively, of seven inferred carotenoid biosynthetic genes, including the genes for phytoene synthase (PSY), phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), ζ-carotene isomerase (Z-ISO), prolycopene isomerase (crtISO), lycopene β-cyclase (LCYB), and lycopene ε-cyclase (LCYE). We found that the evolutionary history of the algal carotenoid biosynthetic pathway was more complex than that of the same pathway in the Streptophyta and, more specifically, that the evolutionary history involved endosymbiotic gene transfer, gene duplication, and gene loss. Almost all of the eukaryotic algae that we examined had inherited the seven carotenoid biosynthesis genes via endosymbiotic gene transfer. Moreover, PSY, crtISO, and the ancestral lycopene cyclase gene (LCY) underwent duplication events that resulted in multiple gene copies, and the duplication and subsequent divergence of LCYB and LCYE specialized and complicated the cyclization of lycopene. Our findings also verify that the loss of LCYE in both the microphytic rhodophytes and phaeophytes explains the differences in their carotenoid patterns, when compared to the macrophytic rhodophytes. These analyses provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of carotenoid biosynthetic pathways.


carotenoid biosynthesis algae phylogenetic analysis 


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The authors are grateful to Michael Melkonian from Universität zu Köln for providing transcriptomic data for Glaucophyta, Cryptophyta, and Haptophyta.


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Copyright information

© The Chinese Society of Oceanography and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Shanshan Wang
    • 1
  • Lei Zhang
    • 1
  • Shan Chi
    • 1
  • Guoliang Wang
    • 2
  • Xumin Wang
    • 2
  • Tao Liu
    • 1
  • Xuexi Tang
    • 1
  1. 1.College of Marine Life SciencesOcean University of ChinaQingdaoChina
  2. 2.CAS Key Laboratory of Genome Sciences and Information/Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina

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