Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

Xiao Huang Chen, Ming Kun Yang, Yuan Yuan Li, Zhang Xian Xie, Shu Feng Zhang, Mats Töpel, Shady A. Amin, Lin Lin, Feng Ge, Da Zhi Wang

Research output: Contribution to journalArticlepeer-review


Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

Original languageEnglish (US)
Pages (from-to)102-115
Number of pages14
JournalMarine Life Science and Technology
Issue number1
StateE-pub ahead of print - Feb 3 2023


  • Marine diatoms
  • Proteogenomics
  • Proteome
  • Thalassiosira pseudonana

ASJC Scopus subject areas

  • Biotechnology
  • Oceanography
  • Ecology, Evolution, Behavior and Systematics
  • Aquatic Science


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