PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum

Abstract

Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.

Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum

“…It is thus possible that aASE is an integral part of the gene regulatory network of diatoms. In that regard, a recent computational study described gene co-regulatory networks making advantages of 187 RNAseq datasets generated in P. tricornutum cultures in varying growth conditions 35 . The in silico investigation of allele-specific effects within gene networks of P. tricornurum cultures subjected to variable growth conditions followed by experimental validation should retain much attention and is the scope of future studies in the field.…”

Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

“…Time-Dependent Dynamics of Bacterial HGT Expression Patterns. We also considered whether bacterially derived genes in ochrophyte genomes had specific epigenetic characteristics or expression patterns, focusing on orthologs from P. tricornutum, for which substantial epigenetic (17,50,51) and quantitative geneexpression data are available (52). Considering structure and location, we noted that bacterial HGTs contain fewer introns per average (0.58 per gene) than other genes across the P. tricornutum genome (0.71 per gene, one-way ANOVA P = 0.03); although 107 of 298 (36%) contained at least one intron (SI Appendix, Fig.…”

“…Gene coregulation values were calculated for P. tricornutum genes in published diatom microarray metastudy data (53), and a novel dataset consisting of combat-normalized RNA-seq data from three previously published studies of P. tricornutum gene expression under N, P, and Fe stress (26,52,54,55). Coregulation values were calculated for bacterial HGTs identified by automated analysis, and attributed from MRCA estimations to have been transferred into P. tricornutum only, or an earlier ancestor of pennate diatoms, pennate and polar centric diatoms, basally divergent diatoms, Khakista and Hypogyristea, or all ochrophytes.…”

The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases

“…This is typified by the overexpression of chaperone DnaJ domain containing proteins and Hsp90 like proteins (Supplementary tables S10 and S11). The recent advances in high through output RNA sequencing technologies led to the recent identification of gene co-regulatory networks in P. tricornutum 41 . Genes with overexpression in DNMT5:KOs are enriched within the "salmon" and "steelblue" coregulatory gene modules.…”

“…The 'salmon' module contains genes associated with chloroplast biology as well as amino acid related enzymes which might highlight metabolic defects. The 'steelBlue' regulatory module associates with protein translation as well as nucleotide metabolism and is enriched in genes involved in purine and pyrimidine cellular pathways 41 . Accordingly, some upregulated proteins are involved in ribosome biosynthesis and RNA processing.…”