About the Genome Project

We have updated the Capitella teleta genome assembly hosted on this site; the previous version is no longer available.

The latest release scaffolds the Capitella genome using Micro-C data, resolving the previously reported split of chromosome 3. Protein-coding gene annotations have been lifted over from the prior assembly, preserving the original gene IDs, and a new repeat annotation was generated for this version.

RNA-seq and ATAC-seq datasets have been remapped accordingly, and methylation data is now available for the first time. Note that chromosomes 1, 2, 3, 4, 6, 9, and 10 appear in inverted orientation relative to the initial assembly.

In collaboration with our colleagues at the University of Florida and the Queen Mary University of London, we have sequenced, assembled, and annotated the 244-megabase genome of Capitella teleta.

Briefly, a combination of Oxford Nanopore long reads, Illumina short reads and HiC chromatin conformation capture was performed on genomic DNA isolated from Capitella adults, yielding a final assembly of 476 scaffolds (N50 of 25.2 Mb), including 11 pseudochromosomes corresponding to the ten described chromosomes (chromosome three is split into two pseudochromosomal scaffolds). RNA-seq data from stage-specific Capitella embryos spanning the oocyte to competent larval stages, generated using Illumina sequencing, were used as the basis for transcriptome annotation. Based on this, the Capitella genome is predicted to contain 26,591 protein-coding genes. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was employed to perform open chromatin profiling and identify potential genome cis-regulatory elements at five developmental time points. In addition, single-cell RNA-seq profiling at two early larval stages facilitates characterization of the cell-type repertoire in Capitella.

For additional information, comments, or questions regarding the Capitella Genome Project, please contact Dr. Baxevanis at andy@nhgri.nih.gov, Professor Seaver at seaver@whitney.ufl.edu, and Dr. Martin at chema.martin@qmul.ac.uk.

Capitella Genome Project Team

Division of Intramural Research, National Human Genome Research Institute, NIH

Computational Genomics Unit

• Andy Baxevanis, Ph.D., Head
• Paul Gonzalez, Ph.D.

Bioinformatics and Scientific Programming Core

• Tyra Wolfsberg, Ph.D., Associate Director
• Travis Moreland, M.S.
• Sumeeta Singh, M.S.
• Suiyuan Zhang, M.S.
• Reynold Yu, Ph.D.
• Mark Fredriksen
• David Kanney, M.B.A.

Whitney Laboratory for Marine Bioscience, University of Florida

• Elaine Seaver, Ph.D.

School of Biological and Behavioural Sciences, Queen Mary University of London

• Chema Martin, Ph.D., Professor
• Billie Davies, Ph.D.
• Tom Frankish
• Jingcheng Wei

Primary Publication on the Capitella teleta Genome Project

In any work or product derived from this material, proper attribution of the authors as the source of the software, database, or data should be made, using the following manuscript as the citation:

• Davies, B.E., Gonzalez, P., Sur, A., Wei, J., Frankish, T., Montagne, J., Carrillo-Baltodano, A.M., Guynes, K., Liang, Y., Donnellan, R.D., Travis Moreland, R., Singh, S., Zhang, S., Wolfsberg, T.G., Meyer, N.P., Seaver, E.C., Baxevanis, A.D., Martín-Durán, J.M. (2026) A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta. Genome Biol Evol. doi: 10.1093/gbe/evag041. [Oxford Academic Open Access]
• Davies, B.E., Martin-Zamora, F.M., Frankish, T., Parey, E., Ellis, N., Maziak, N., Guynes, K., Zolotarov, G., Luo, Y.J., Marletaz, F., Vaquerizas, J.M., Sebe-Pedros, A., Zabet, N.R., Hurd, P.J., and Martin-Duran, J.M. (2026). Convergent evolution of cluster-wide Hox gene regulation in Bilateria. bioRxiv. [https://www.biorxiv.org/content/10.64898/2026.05.18.725834v1] .