期刊
MOLECULAR PLANT
卷 11, 期 10, 页码 1292-1307出版社
CELL PRESS
DOI: 10.1016/j.molp.2018.08.005
关键词
Phaeodactylum tricornutum; proteogenomics; mass spectrometry; genome annotation
资金
- National Key Research and Development Program [2016YFA0501304]
- National Natural Science Foundation of China [31570829]
- Strategic Priority Research Program of the Chinese Academy of Sciences [XDB14030202]
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that significantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the development of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry (MS)-based proteomics data. Our proteogenomic analysis unambiguously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricornutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis.
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