The genome assembly of the duckweed fern, Azolla caroliniana - PubMed (original) (raw)

. 2025 Aug 23;116(5):691-701.

doi: 10.1093/jhered/esaf022.

Yanã C Rizzieri 2 3, Fay-Wei Li 2 3, Forrest Freund 4, Merly Escalona 5, Erin Toffelmier 6 7, Courtney Miller 6, H Bradley Shaffer 6 7, Oanh Nguyen 8, Mohan P A Marimuthu 8, Noravit Chumchim 8, Carrie Tribble 9, Colin W Fairbairn 10, William Seligmann 10, Carl J Rothfels 11 12

Affiliations

The genome assembly of the duckweed fern, Azolla caroliniana

Michael J Song et al. J Hered. 2025.

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 2 species are currently recognized but the actual diversity may include up to 6 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 and annotation 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 pseudochromosomes. A total of 21,848 protein-coding genes was predicted with a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 89.88%. In combination with the previously published Azola 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.

Keywords: Azolla; CCGP; California Conservation Genomics Project; HiFi; Omni-C; diploid genome assembly; reference genome.

© The American Genetic Association. 2025.

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Figures

Fig. 1.

Fig. 1.

Azolla caroliniana from the genome-sample collection site: Lake Anza, Tilden Regional Parks, Contra Costa County, California. a) Habitat; b) microsporocarp with glochidia at 200×; c) Whole-plant abaxial surface; d) megasporocarps showing megaspores; e) close up of adaxial leaf surface; f) whole-plant adaxial surface. Photo credit: Forrest Freund.

Fig. 2.

Fig. 2.

Azolla caroliniana chromosome-level genome assembly. a) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome and the k-mer profile matches that of high heterozygosity. b) Omni-C contact maps for the curated genome assembly of haplotype 1 generated with PretextSnapshot. Omni-C contact maps translate the proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between 2 of such regions. Scaffolds are separated by black lines. c) Haplotype 1 and d) haplotype 2 BlobToolKit snail plot showing a graphical representation of the quality metrics presented in Table 2. The first diagonal (~30 °C) line represents the size of the longest scaffold; all other scaffolds are arranged in order of size clockwise around the plot and drawn in gray starting from the outside of the central plot. The inner arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly; the outer dark vs. light area around it shows mean, maximum, and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020).

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