Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species

BACKGROUND

Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies.

RESULTS

The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2-3.7% of the total genome depending on the pairwise comparison of references. In addition, unsupported higher order scaffolding was identified in published reference genomes. In contrast, we estimated 8.2% of the compared narwhal genomes featured discrepancies, with inversions being notably abundant (5.3%). Discrepancies were linked to repetitive elements in both species.

CONCLUSIONS

We provide several new reference genomes for beluga (Delphinapterus leucas), while highlighting potential avenues for improvements. In particular, additional layers of data providing information on ultra-long genomic distances are needed to resolve persistent errors in reference genome construction. The comparative analyses of monodontid reference genomes suggested that the three new reference genomes for beluga are more accurate compared to the currently published reference genome, but that the new narwhal genome is less accurate than one published. We also present a conceptual summary for improving the accuracy of reference genomes with relevance to end-user needs and how they relate to levels of assembly quality and uncertainty.

Prolonged baleen hormone cycles suggest atypical reproductive endocrinology of female bowhead whales

Serial measurements of hormone concentrations along baleen plates allow for reconstructions of mysticete whale reproductive histories. We assessed gestation and calving interval in bowhead whales (Balaena mysticetus) by measuring progesterone, oestradiol, corticosterone and nitrogen stable isotope ratios (δ¹⁵N) along baleen of 10 females from the eastern Canada-west Greenland population. Three immature females (body size < 14.32 m) had uniformly low progesterone concentrations across their baleen, while seven mature females (body size ≥ 14.35 m) had repeated, sustained elevations of progesterone indicative of pregnancies. The mean duration of progesterone elevations (23.6 ± 1.50 months) was considerably longer than the approximately 14 month gestation previously estimated for this species. We consider several possible explanations for this observation, including delayed implantation or sequential ovulations prior to gestation, strategies that would allow females to maximize their fitness in variable Arctic conditions, as well as suggest modified criteria defining gestation as a shorter component of the entire progesterone peak. Calving intervals varied within and among individuals (mean = 3.7 years; range = range 2.8-5.7 years), providing population-specific reproductive estimates for growth models used in bowhead whale management and conservation.

Wax-wetting sponges for oil droplets recovery from frigid waters

Energy-efficient recovery of oil droplets from ice-cold water, such as oil sands tailings, marine, and arctic oil spills, is challenging. In particular, due to paraffin wax crystallization at low temperatures, the crude oil exhibits high viscosity, making it difficult to collect using simple solutions like sponges. Here, we report a wax-wetting sponge designed by conforming to the thermoresponsive microstructure of crude oil droplets. To address paraffin wax crystallization, we designed the sponge by coating a polyester polyurethane substrate with nanosilicon functionalized with paraffin-like octadecyl ligands. The wax-wetting sponge can adsorb oil droplets from wastewater between 5° and 40°C with 90 to 99% removal efficacy for 10 cycles. Also, upon rinsing with heptol, the adsorbed oil is released within seconds. The proposed approach of sponges designed to conform with the temperature-dependent microstructure of the crude oils could enable cold water technologies and improve circular economy metrics in the oil industry.