Phylogenomic pipeline for uncultivable microbial eukaryotes using single cell RNA sequencing data - A case study with planktonic ciliates (Protista, Ciliophora, Oligotrichea).

We collected marine planktonic ciliates from a dock located in Groton, Connecticut, USA. The collection was made on multiple dates from July 2020 to January 2022. After isolating the single cell, we performed single-cell RNA sequencing. We created a phylogenomic pipeline relying on PhyloTol to construct single gene trees from the transcriptomic data. Our pipeline produced well-curated data, which we used to estimate species trees. Overall this project provides a guideline to infer species tree of uncultivable microbial eukaryotes using single cell RNA sequencing data.