The complete genome of a songbird

Formenti, G.; Jain, N.; Medico, J. A.; Sollitto, M.; Antipov, D.; Balacco, J.; Barcellos, S.; Biegler, M. T.; Borges, I.; Chang, J. K.; Chen, Y.; Cheng, H.; Conceicao, H. B.; Davenport, M.; De Oliveira, L. C.; Duarte, E.; Durham, G. P.; Fenn, J.; Forde, N.; Kim, J.; Komissarov, A.; Koo, B.; Koren, S.; Galante, P. A. F.; Gerhardt, K.; Giani, A. M.; Giunta, S.; Larkin, D.; Lee, C.; Li, H.; Makova, K.; Masterson, P.; Murphy, T.; McCaffrey, K.; Mercuri, R. L. V.; Na, Y.; O Connell, M. J.; Ou, S.; Phillippy, A. M.; Popova, M.; Rhie, A.; Ruiz-Ruano, F. J.; Secomandi, S.; Smeds, L.; Suh, A.; Tilley,

doi:10.1101/2025.10.14.682431

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bioRxiv · 10.1101/2025.10.14.682431

The complete genome of a songbird

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Abstract

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding [~]90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

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Formenti, G., Jain, N., Medico, J. A., Sollitto, M., Antipov, D., Balacco, J., Barcellos, S., Biegler, M. T., Borges, I., Chang, J. K., Chen, Y., Cheng, H., Conceicao, H. B., Davenport, M., De Oliveira, L. C., Duarte, E., Durham, G. P., Fenn, J., Forde, N., Kim, J., Komissarov, A., Koo, B., Koren, S., Galante, P. A. F., Gerhardt, K., Giani, A. M., Giunta, S., Larkin, D., Lee, C., Li, H., Makova, K., Masterson, P., Murphy, T., McCaffrey, K., Mercuri, R. L. V., Na, Y., O Connell, M. J., Ou, S., Phillippy, A. M., Popova, M., Rhie, A., Ruiz-Ruano, F. J., Secomandi, S., Smeds, L., Suh, A., Tilley,. 2025-10-14. The complete genome of a songbird. https://doi.org/10.1101/2025.10.14.682431

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