title: Single-cell transcriptomics for microbial eukaryotes.
abstract: One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity.
authors.affiliation: Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Kolisko
authors.affiliation: Biology Department, University of Pisa, via Alessandro Volta 4/6, Pisa, 56126, Italy.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Boscaro
authors.affiliation: Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Fabien
authors.initials: F
authors.lastname: Burki
authors.affiliation: Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Denis H
authors.initials: DH
authors.lastname: Lynn
authors.affiliation: Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada. Electronic address: pkeeling@mail.ubc.ca.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
mesh_terms: D044822:Biodiversity; D048429:Cell Size; D056890:Eukaryota / Q000166:cytology / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D059010:Single-Cell Analysis; D059467:Transcriptome