The origin and evolution of archaeal Borg extrachromosomal elements

Shi, L.-D.; Penev, P.; Kolody, B. C.; Miloslavich, L.; Lei, S.; Sachdeva, R.; Rasmussen, A. N.; Tolar, B. B.; Francis, C. A.; Probst, A. J.; Vazquez-Campos, X.; Payne, T. E.; Jiang, Z.; Li, J.; Wang, C.; He, Z.; Ni, J.; Hug, L. A.; Banfield, J.

doi:10.64898/2026.05.22.727314

bioRxiv · 10.64898/2026.05.22.727314

The origin and evolution of archaeal Borg extrachromosomal elements

Shi, L.-D.·Penev, P.·Kolody, B. C.·Miloslavich, L.·Lei, S.·Sachdeva, R.·Rasmussen, A. N.·Tolar, B. B.·Francis, C. A.·Probst, A. J.·Vazquez-Campos, X.·Payne, T. E.·Jiang, Z.·Li, J.·Wang, C.·He, Z.·Ni, J.·Hug, L. A.·Banfield, J.

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Abstract

Borgs are giant linear extrachromosomal elements (ECEs) of methane-oxidizing Methanoperedens archaea whose evolutionary origin and ecosystem distribution remain unknown. Here we detected 240 Borgs in diverse saline, soil, and freshwater ecosystems. 27 encode methyl-coenzyme M reductases central to methane metabolism, eight have full rRNA operons related to those of Methanoperedens, and some contain up to four ribosomal proteins. We also identified 323 mini-Borgs whose proteome content and gene phylogenies classify as a distinct ECE type. Based on 105 complete and near-complete genomes, Borgs and mini-Borgs share core genes in conserved order, indicating common ancestry. Phylogenetic and diversity analyses suggest that Borgs evolved via gene acquisition into a backbone inherited from mini-Borgs. This evolutionary trajectory mirrors those proposed for giant viruses of both eukaryotes and bacteria.

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Shi, L.-D., Penev, P., Kolody, B. C., Miloslavich, L., Lei, S., Sachdeva, R., Rasmussen, A. N., Tolar, B. B., Francis, C. A., Probst, A. J., Vazquez-Campos, X., Payne, T. E., Jiang, Z., Li, J., Wang, C., He, Z., Ni, J., Hug, L. A., Banfield, J.. 2026-05-23. The origin and evolution of archaeal Borg extrachromosomal elements. https://doi.org/10.64898/2026.05.22.727314

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