Survival in a changing world: The role of transcriptomics and the urgent need for genomes to understand Arcellinida’s adaptive capabilities

Understanding the physiological and genetic diversity of single-cell eukaryotes remains a big challenge for scientists. Single-cell omics technologies have revolutionized our possibilities for many previously uncharacterized groups. Despite the great advancement, there is still a substantial gap in our genomic knowledge about eukaryotes, with less than 1% of species sequenced. This knowledge gap is even more pronounced in some microbial eukaryote groups such as Arcellinids. Arcellinida is a group of bioindicator protists that inhabit mostly freshwater and soil environments. Currently, we don’t have any genome available for the Arcellinida group, undermining our capacity to understand their biology, metabolic capacities, and resistance mechanisms that makes them useful as bioindicators. Using transcriptomic data only, we made great progress in this group by elucidating, for example, their systematics, sex, and metabolism. This manuscript highlights the potential of Arcellinida as a model for genomic studies, particularly the Arcella uspiensis species. Through comparative analysis, we demonstrate that despite its importance, transcriptomics hinders some limitations that need to be acknowledged. Finally, considering that we have much basic biology knowledge and protocols for Arcella uspiensis, we propose sequencing the genome of this species as a way to unlock further potential insights into ecology, evolution, and function of Arcellinida. This manuscript emphasizes the importance of exploring genomics as a way to understand the ecology and evolution of microbial eukaryotic groups.