Arcella uspiensis

Arcella uspiensis as a prime candidate for genome sequencing projects in Arcellinida

Arcella uspiensis is a potential model organism to start genomic studies due to its high representation in different environments, relevance as a bioindicator, ability to grow in cultures, and highly developed protocols for this lineage. Currently, Arcella uspiensis is one of the Arcellinids with the most available data, describing their ecological and evolutionary process, metabolism, and resistance capacities. Arcella uspiensis is an Arcellinida View in CoL species for which it is possible to establish stable cultures and from whom there is already a lot of basic biology and protocols knowledge until now ( Fig. 3 View Fig ). Different problematics in ecology and evolution were already tested and studied with these cultures. For example, Arcella uspiensis is currently an example of phenotypic plasticity in Arcellinids, considering that Porfírio‑Sousa and Ribeiro, 2017 showed two different morphotypes of Arcella View in CoL were the same genetic unity ( Porfírio-Sousa et al. 2017). In this same paper, it was also observed that the shape of the shells changed when they were moved from the environment into cultures. Community-level studies, such as the works of Nasser and Patterson, already inform us about the different degrees of resistance among Arcellinids ( Nasser et al. 2016; Patterson et al. 2019). These studies show us that Arcella View in CoL specimens usually occur in various kinds of environments such as eutrophic, saline, and contaminated by arsenic. Metabarcoding studies also showed Arcella species occupying saline environments ( Useros et al. 2023). Although we have plenty of ecological studies on this species, we still have not clarified by experimen- tal evidence their adaptative capabilities. Relying only on transcriptomic data, comparative analysis already found potential markers of adaptative capabilities in Arcella uspiensis . Ribeiro et al. described general Arcella uspiensis metabolism based on culture transcriptomic data, and Ribeiro and Lahr described arsenic resistance metabolism using our current transcriptomic database ( Ribeiro et al. 2020; Ribeiro and Lahr 2022). Based on this works, genes related to arsenic resistance were found in Arcella uspiensis , but genomic data would enable us to discover the complete pathways and untangle the functional analysis regarding arsenic resistance metabolisms.

Considering the importance of genomic data, why are there still no genomes for Arcellinids? One of the main difficulties is that considering they are single‑cell organisms, many species do not grow in cultures, and many species are not that abundant in the environment; having enough DNA for sequencing the complete genome is much more complicated to develop with this group. Considering this issue, Arcella View in CoL would be a good model to start. It is possible to consistently grow Arcella uspiensis in cultures, generating a higher number of cells for DNA extractions. Additionally, there are already protocols in different areas of investigation op- timized to work on this group ( Fig. 3 View Fig ). For example, Ribeiro et al. 2019 described the culture and growth cultures protocol developed with Arcella uspiensis ( Ribeiro et al. 2019) . Another example, Porfirio‑Sousa et al. recently developed a protocol to die cytoskeleton components using immunocytochemistry ( Porfirio‑Sousa et al. 2023). These protocols have a lot of relevance because they are replicable, and, used together with genomes, should enable us to understand the effect of an environmental condition on the growth of the amoebae population in culture, mark specific proteins for localization, and further analyze the expression pattern by transcriptomics. In summary, after all that was already developed using Arcella uspiensis , we believe that because within this group, we have a lot of biological information available, we already have many transcriptomes produced, and we have a lot of molecular biology and growth cultures protocols established for this group, building their genomes is the next logical step.