A Genome for Bidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation

Abstract

The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. The 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, of which many are imperiled and of high conservation concern. Until now, no genomic resources were available for this genus, which may serve as a model system for understanding the evolutionary genomics of explosive plant diversification. Here, we present a high-quality reference genome for the Hawai'i Island endemic species B. hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences generated on a Pacific Biosciences Sequel II System. The haplotype-aware, draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the holoploid genome size estimate of 7.56 Gb (±0.44 SD) determined by flow cytometry. After removal of alternate haplotigs and contaminant filtering, the consensus haploid reference genome was comprised of 15 904 contigs containing ~3.48 Gb, with a contig N50 value of 422 594. The high interspersed repeat content of the genome, approximately 74%, along with hexaploid status, contributed to assembly fragmentation. Both the haplotype-aware and consensus haploid assemblies recovered >96% of Benchmarking Universal Single-Copy Orthologs. Yet, the removal of alternate haplotigs did not substantially reduce the proportion of duplicated benchmarking genes (~79% vs. ~68%). This reference genome will support future work on the speciation process during adaptive radiation, including resolving evolutionary relationships, determining the genomic basis of trait evolution, and supporting ongoing conservation efforts.

Keywords: Asteraceae; PacBio HiFi; flow cytometry; koʻokoʻolau; monoploid genomes; polyploid.

Figure 1.

A profile of Bidens hawaiensis. (a) A B. hawaiensis flower photographed from the plant used for flow cytometry and genome sequencing. (b) An example flow cytometry data plot from one replicate of a sample with both Lycopersicon esculentum and B. hawaiensis. Shown are the number of nuclei as a function of the DNA fluorescence (arbitrary units) from propidium iodide staining. Data for the mean peak position of each replicate sample (n = 10) are available from Supplementary Table 2. (c, d) K-mer spectrum analysis of HiFi data. (c) The 3 monoploid genomes of B. hawaiensis can be detected as peaks in the coverage ∗ frequency plot. (d) A plot showing that a dominant k-mer frequency peak occurs at approximately 12x coverage, and that numerous k-mers with modest coverage were miscategorized as sequencing errors.

Figure 2.

Comparative assessments of genome completeness and size. The genome assembly comparisons include the hexaploid Ko’oko’olau (Bidens hawaiensis; haploid consensus assembly), 12 diploid Asteraceae, and 5 polyploid eudicots (ploidy number in parenthesis). (a) Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis with the eudicot ODB10 database containing 2326 genes. Shown are the proportion and numbers of BUSCO gene recoveries categorized as complete and single-copy (S), complete and duplicated (D), fragmented (F), or missing (M). (b) Total number of assembled bases for each genome. See Supplementary Table 1 for scientific names, genome accessions (when available), and genome references.