Recent Advances in Application of Transcriptomics: Research on Heterotrophic and Autotrophic Protists

Abstract

The application of molecular phylogenetics to research on protists has substantially transformed our understanding of their evolution and systematics. More recently, advances in molecular technology, including high throughput sequencing, has opened new avenues for genomic analyses that elucidate major aspects of protistan biology across all levels of biological organization from cellular to ecosystems. This is a review of recent advances (particularly in the last two decades) of transcriptomic research on heterotrophic and autotrophic protists within three major topics: (i) Physiology and metabolism, (ii) Development and life cycles, and (iii) Environmental and ecological studies. Emphasis is placed on selection of representative research that highlights findings across diverse taxonomic groups within each of the three topics. Examples are drawn from parasitic as well as free-living taxa to provide a broad overview of some of the research strategies, and major findings, that have emerged from application of transcriptomics and related techniques in advancing our understanding of protistan biology.

Missing microbial eukaryotes and misleading meta-omic conclusions

“…Because genetic data are often collected when cell densities and expression levels are high, expression profiles may be most similar to when the microorganism is dominant and abundant in the field. Moreover, reference datasets that include different cell life cycle stages and environmental conditions would be ideal to link taxonomic identity to functional role but are not always available 30 .…”

Transcriptome analysis reveals the molecular mechanism of differences in growth between photoautotrophy and heterotrophy in Chlamydomonas reinhardtii

“…In previous studies, the transcriptome was widely used in heterotrophic and autotrophic microalgae including physiology and metabolism, development and life cycles, environmental and ecological studies [33]. In this study, the transcriptomics analysis was estimated for samples from photoautotrophy (P12h) and heterotrophy (H12h).…”

“…Transcriptome analyses contributed to nding the target genes and pathways that could be the focus of further physiological and molecular research [14]. Recent studies have summarized recent advances in transcriptomic research on heterotrophic and autotrophic protists, including physiology and metabolism, development and life cycles, environmental and ecological studies [15]. However, there is little research focus on the transcriptome comparing the growth differences between Chlamydomonas rheinensis under autotrophic and heterotrophic conditions.…”

DataSheet_1.docx

“…In previous studies, the transcriptome was widely used in heterotrophic and autotrophic microalga, including physiology and metabolism, development and life cycles, environmental and ecological studies (Anderson, 2022b). In this study, the transcriptomics analysis was estimated for samples from photoautotrophy (P12h) and heterotrophy (H12h) (Figure 2).…”

“…Transcriptome analysis contributed to finding target genes and pathways that could be the focus of further physiological and molecular studies (Dong et al, 2023). Recent studies have summarized advances in transcriptomic research on heterotrophic and autotrophic protists, including physiology and metabolism, development and life cycles, environmental and ecological studies (Anderson, 2022a).…”