Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing − A case study with planktonic ciliates (Ciliophora, Oligotrichea)

[Display omitted] •Twenty-eight new single-cell transcriptomes for Oligotrichea ciliates.•Phylogenomic workflow from single cell isolation to species tree inference.•Asteroid robustly infers species tree in the presence of paralogs and missing data. Phylogenetic analyses increasingly rely on genomic...

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