NUMT (Nuclear-mitochondrial DNA segment) annotation release 2024/10-03
NUMTs were annotated using blastn (version 2.6.0) to align mitochondrial DNA assemblies to nuclear assemblies of the same species. These species include T2T apes at the time of release (including human CHM13). Overlapping NUMTs were merged using bedtools (version 2.30.0). The code can be found in Github: (https://github.com/makovalab-psu/T2T_primate_autosomes/tree/main/Detection_of_NUMTs).
Kateryna Makova<kdm16@psu.edu>, Edmundo Torres-Gonzalez
Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechova, M., Pal, K., Nurk, S., Yoo, D., Li, Q., Hebbar, P., McGrath, B. C., Antonacci, F., Aubel, M., Biddanda, A., Borchers, M., Bornberg-Bauer, E., Bouffard, G. G., Brooks, S. Y., Carbone, L., Carrel, L., … Phillippy, A. M. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature, 630(8016), 401–411. https://doi.org/10.1038/s41586-024-07473-2
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., Caldas, G. V., … Phillippy, A. M. (2022). The complete sequence of a human genome. Science (New York, N.Y.), 376(6588), 44–53. https://doi.org/10.1126/science.abj6987
Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., Allen, J., Asri, M., Bzikadze, A. V., Chen, N. C., Chin, C. S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Garcia Giron, C., … Phillippy, A. M. (2023). The complete sequence of a human Y chromosome. Nature, 621(7978), 344–354. https://doi.org/10.1038/s41586-023-06457-y
Yoo, D. A., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J. M., Lin, J., Sequeira, A. N., Mangan, R. J., Hickey, G., Monfort Anez, G., Balachandran, P., ... Eichler, E. E. (2024). Complete T2T-CHM13 assembly reveals new insights into centromere biology. bioRxiv. https://doi.org/10.1101/2024.07.31.605654