Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline

Abstract

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. The pipeline and its source code are freely available at https://sourceforge.net/projects/gapeproteogenomic.

Systematic and functional analysis of horizontal gene transfer events in diatoms

“…they claimed that most influx occurred at ancestor of the photosynthetic Stramenopiles (Ochrophytes), 60 while our results indicate this happened more recently in the ancestor of the diatom clade. 61…”

“…Given that most HGT genes are kept under purifying selection 216 in P. tricornutum and are transcribed in diatoms, this is indicative that they are functional and can play 217 a vital role in expanding the functional repertoire. Indeed, 64% of the predicted HGT genes in P. 218 tricornutum were translated into proteins in a proteogenomic analysis 60 . This is similar to 63% of all 219 proteins in the genome that were detected to be translated.…”

Proteome-Wide Identification of Lysine Propionylation in the Conidial and Mycelial Stages of Trichophyton rubrum

“…The raw proteome data were downloaded from Peptide Atlas with the dataset identifier PASS01111 (Xu et al, 2018a). We performed the combined unrestrictive searching strategy using MODa (version 1.23) (Na et al, 2012) and the specific PTM searching approach using MaxQuant (version 1.6.0.16) (Cox and Mann, 2008) as previously described (Yang et al, 2018). A total of 26 PTMs were selected to search for their possible presence in T. rubrum .…”

Diatoms’ Breakthroughs in Biotechnology: <i>Phaeodactylum tricornutum</i> as a Model for Producing High-Added Value Molecules

“…In the . Key events related to diatoms including P. tricornutum and T. pseudonana species: First P. tricornutum transformation [72], First P. tricornutum cloning [73], T. pseudonana's whole genome sequence [31], P. tricornutum's whole genome sequence [45], First RNA silencing in P. tricornutum [53], T. oceanica's genome sequencing [69], First CRISPR in P. tricornutum [74] and T. pseudoana [75], Genome sequence of Pseudo-nitzschia multistriata [71], Reannotaion of P. tricronutum's genome sequence [76], Nanofrustulum shiloi's chloroplast genome sequence [77]. macronucleus, proteins transcription takes place, while the germline micronucleus is silenced.…”