The genome assembly of the duckweed fern, Azolla caroliniana

Song, M. J.; Li, F.-W.; Freund, F.; Escalona, M.; Toffelmier, E.; Miller, C.; Shaffer, H. B.; Nguyen, O.; Marimuthu, M. P. A.; Chumchim, N.; Tribble, C.; Fairbairn, C. W.; Seligmann, W.; Rothfels, C. J.

doi:10.1101/2024.10.22.619683

bioRxiv · 10.1101/2024.10.22.619683

The genome assembly of the duckweed fern, Azolla caroliniana

Song, M. J.·Li, F.-W.·Freund, F.·Escalona, M.·Toffelmier, E.·Miller, C.·Shaffer, H. B.·Nguyen, O.·Marimuthu, M. P. A.·Chumchim, N.·Tribble, C.·Fairbairn, C. W.·Seligmann, W.·Rothfels, C. J.

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Abstract

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only two species are currently recognized but there may be up to six putative species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies. The assembly is 521 Mb in length, with a contig N50 of 1.6 Mb, and is scaffolded into 22 pseudo-chromosomes. The BUSCO completeness score is 87.5%, making it the most complete and most contiguous Azolla assembly to date. In combination with the previously published A. filiculoides genome, this A. caroliniana genome will be a powerful tool for understanding the population genetics and taxonomy of one of the most cryptic, economically important, and poorly circumscribed fern taxa, and for facilitating land plant genomics more broadly.

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Song, M. J., Li, F.-W., Freund, F., Escalona, M., Toffelmier, E., Miller, C., Shaffer, H. B., Nguyen, O., Marimuthu, M. P. A., Chumchim, N., Tribble, C., Fairbairn, C. W., Seligmann, W., Rothfels, C. J.. 2024-10-25. The genome assembly of the duckweed fern, Azolla caroliniana. https://doi.org/10.1101/2024.10.22.619683

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