Data from: Morphological identification and single-cell genomics of marine diplonemids

Recent global surveys of marine biodiversity have revealed that a group of
organisms known as “marine diplonemids” constitutes one of the most
abundant and diverse planktonic lineages [1]. Though discovered over a
decade ago [2 and 3], their potential importance was unrecognized, and our
knowledge remains restricted to a single gene amplified from environmental
DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell
genomics (SCG) and microscopy to characterize ten marine diplonemids,
isolated from a range of depths in the eastern North Pacific Ocean.
Phylogenetic analysis confirms that the isolates reflect the entire range
of marine diplonemid diversity, and comparisons to environmental SSU
surveys show that sequences from the isolates range from rare to
superabundant, including the single most common marine diplonemid known.
SCG generated a total of ∼915 Mbp of assembled sequence across all ten
cells and ∼4,000 protein-coding genes with homologs in the Kyoto
Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed
across categories expected for heterotrophic protists. Models of highly
conserved genes indicate a high density of non-canonical introns, lacking
conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG
assemblies reveals virtually no overlap, suggesting that nuclear genomic
diversity is too great for representative SCG data to provide meaningful
phylogenetic context to metagenomic datasets. This work provides an entry
point to the future identification, isolation, and cultivation of these
elusive yet ecologically important cells. The high density of
nonconventional introns, however, also portends difficulty in generating
accurate gene models and highlights the need for the establishment of
stable cultures and transcriptomic analyses.