Gene Expression Patterns in the Ctenophore Pleurobrachia bachei: In Situ Hybridization

Methods Mol Biol. 2024:2757:215-237. doi: 10.1007/978-1-0716-3642-8_9.


In situ hybridization is a powerful and precise tool for revealing cell- and tissue-specific gene expression and a critical approach to validating single-cell RNA-seq (scRNA-seq). However, applying it to highly fragile animals such as ctenophores is challenging. Here, we present an in situ hybridization protocol for adult Pleurobrachia bachei (Cydippida)-a notable reference species representing the earliest-branching metazoan lineage, Ctenophora, sister to the rest of Metazoa. We provided expression patterns for several markers of cell phenotypes, as illustrated examples. The list includes predicted small secretory molecules/neuropeptides, WntX, genes encoding RNA-binding proteins (Musashi, Elav, Dicer, Argonaut), Neuroglobin, and selected transcription factors such as BarX. Both cell- and organ-specific expression of these genes further support the convergent evolution of many ctenophore innovations, which are remarkably distinct from tissue and organ specification in other basal metazoan lineages.

Keywords: Argonaut; Ctenophores; Dicer; ELAV; Evolution; Gene expression; Genome; In situ hybridization; Mnemiopsis; Musashi; Neuroglobin; Neurons; Neuropeptides; Pleurobrachia; Wnt signaling.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Ctenophora* / genetics
  • Ctenophora* / metabolism
  • Gene Expression Profiling / methods
  • In Situ Hybridization* / methods