biostudies-literatureZhao WEarmarked Fund for China Agriculture Research SystemChina Postdoctoral Science FoundationNational Natural Science Foundation of ChinaSecond Tibetan Plateau Scientific Expedition and Research Program (STEP)National Key Research and Development Program of ChinaNational Natural Science Foundation of China (National Science Foundation of China)323https://www.ebi.ac.uk/biostudies/studies/S-EPMC10978948biostudies-literatureUnknown11(1)Balantidium ctenopharyngodoni is identified as the sole ciliate species that exclusively resides within the hindgut of grass carp with high prevalence and intensity. In this study, the successful cultivation of B. ctenopharyngodoni enabled us to collect enough cells for genome sequencing. Consequently, we acquired a high-quality genome assembly spanning 68.66 Mb, encompassing a total of 22,334 nanochromosomes. Furthermore, we predicted 29,348 protein-coding genes, and 95.5% of them was supported by the RNA-seq data. The trend of GC content in the subtelomeric regions of single-gene chromosomes was similar to other ciliates containing nanochromosomes. A large number of genes encoding carbohydrate-binding modules with affinities for starch and peptidoglycans was identified. The identificatioScientific dataGenome assembly of a symbiotic balantidia (Balantidium ctenopharyngodoni) in fish hindgut.PMC109789482021M70343532170437CARS-4532303066Li WZou HXiong JBu XChen KZhang JZhao WJiang CWang GMiao WLi MfalseGenome assembly of a symbiotic balantidia (Balantidium ctenopharyngodoni) in fish hindgut.Balantidium ctenopharyngodoni is identified as the sole ciliate species that exclusively resides within the hindgut of grass carp with high prevalence and intensity. In this study, the successful cultivation of B. ctenopharyngodoni enabled us to collect enough cells for genome sequencing. Consequently, we acquired a high-quality genome assembly spanning 68.66 Mb, encompassing a total of 22,334 nanochromosomes. Furthermore, we predicted 29,348 protein-coding genes, and 95.5% of them was supported by the RNA-seq data. The trend of GC content in the subtelomeric regions of single-gene chromosomes was similar to other ciliates containing nanochromosomes. A large number of genes encoding carbohydrate-binding modules with affinities for starch and peptidoglycans was identified. The identificatio2024-01-01T00:00:00Z2024 Mar2026-06-01T21:47:24.718Z2025-04-04T19:12:25.385ZS-EPMC109789483854875510.1038/s41597-024-03142-1