Comparative Transcriptome Analysis of Four Prymnesiophyte Algae

Abstract

Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.

Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

“…They were affiliated with metabolic pathways including translation and ribosomal biogenesis, transcription and protein processing as well as with pathways affiliated with "Carbohydrate metabolism", "Lipid metabolism", "Nucleotide metabolism", "Amino acid metabolism" and "Signal transduction". This corresponds well with transcriptomic studies of other taxa which revealed a similar number and affiliation of genes of the core transcriptome with metabolic pathways (prymnesiophytes 1,433 core genes: Koid et al 2014; diatoms 1,370 core genes: Di Dato et al 2015). This proves the general importance of these pathways for taxa affiliated with various groups of Eukaryota.…”

“…In our study we also tested such a sequence based method but in contrast to the results of Liu et al (2016) and Koid et al (2014) we could not identify a higher number of core genes. Genome based studies of related lineages also range from 1,666 to 3,063 core genes (Bowler et al 2008, Radakovits et al 2012.…”

“…This seems low but is similar in size to core transcriptomes reported for prymnesiophytes (Koid et al 2014: 1,433 core genes) and diatoms (Di Dato et al 2015: 1,370 core genes); all these estimates are based on functionally assignable genes. Sequence based methods for the identification of core genes are independent from the necessity of functional assignment and resulted in previous studies in approximately 3,000 core genes (Liu et al 2016, Koid et al 2014). …”

“…Koid et al (2014) already pointed out that genes which are not part of the basal metabolism or more specific to distinct taxonomic groups often cannot be identified with respect to their function. Further, Fuhrman (2009) assumed that amongst the non-core genes with unknown function are those genes that are responsible for niche adaption.…”

“…the transcriptome, investigations of core genes are scarce. Estimates on the core transcriptome within a lineage to date indicate a core set of at least 1,400 to 3,000 genes (Koid et al 2014, Beisser et al 2017, Liu et al 2016). Here we focus on the comparative transcriptomics of members of Ochromonadales (Chrysophyceae) aiming at the genetic repertoire essential for chrysophytes.…”