BackgroundThe Tunicata or Urochordata is the only animal group with the ability to synthesize cellulose directly and cellulose is a component of the tunic that covers the entire tunicate body. The genome ofCiona intestinalistype A contains a cellulose synthase gene,CesA,that it acquired via an ancient, horizontal gene transfer.CesAis expressed in embryonic epidermal cells and functions in cellulose production.CionaCesA is composed of both a glycosyltransferase domain, GT2, and a glycosyl hydrolase domain, GH6, which shows a mutation at a key position and seems functionless. Interestingly, theCionagenome contains a glycosyl hydrolase gene,GH6-1,in which the GH6 domain seems intact. This suggests expression and possible functions ofGH6-1duringCionaembryogenesis. IsGH6-1expressed during embryogenesis? If so, in what tissues is the gene expressed? DoesGH6-1serve a function? If so, what is it? Answers to these questions may advance our understanding of evolution of this unique animal group.ResultsQuantitative reverse transcription PCR and in situ hybridization revealed thatGH6-1is expressed in epidermis of tailbud embryos and in early swimming larvae, a pattern similar to that ofCesA.Expression is downregulated at later stages and becomes undetectable in metamorphosed juveniles. TheGH6-1expression level is higher in the anterior-trunk region and caudal-tip regions of late embryos. Single-cell RNA sequencing analysis of the late tailbud stage showed that cells of three clusters with epidermal identity expressGH6-1, and that some of them co-expressCesA. TALEN-mediated genome editing was used to generateGH6-1knockoutCionalarvae. Around half of TALEN-electroporated larvae showed abnormal development of adhesive papillae and altered distribution of surface cellulose. In addition, three-fourths of TALEN-electroporated animals failed to complete larval metamorphosis.ConclusionsThis study showed that tunicateGH6-1, a gene that originated by horizontal gene transfer of a prokaryote gene, is recruited into the ascidian genome, and that it is expressed and functions in epidermal cells of ascidian embryos. Although further research is required, this observation demonstrates that bothCesAandGH6-1are involved in tunicate cellulose metabolism, impacting tunicate morphology and ecology.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13227-023-00215-x.