ABOVE: A black abalone near Marina, California © INATURALIST.COM, ALLISONJGONG

Black abalone (Haliotis cracherodii) were once abundant in California’s subtidal habitats, providing protein and lustrous shells to the Indigenous peoples that lived alongside them for millennia. US commercial fisheries initially focused on the herbivorous mollusk’s relatives, but following overharvesting-driven declines in those shellfish, a large-scale commercial fishery for the black abalone began in 1968, which by the early 1970s was pulling hundreds of metric tons of the animals from the coast each year. Then, in the 1980s and 1990s—when the black abalone was already in decline—a devastating microbial disease known as withering syndrome killed millions of them, wiping out more than 80 percent of the total population. This prompted the International Union for Conservation of Nature (IUCN) to designate the species as critically endangered and triggered a flurry of federal protections.

In 2020, the US National Marine Fisheries Service identified eight major actions required to conserve and restore the animals, including evaluating the genetic structure and diversity of wild populations. While some genetics studies on the black abalone had been published, a deeper understanding of the animals’ biology and ecology been hampered by the absence of genomics resources. So, to aid such work as well as to provide novel insights into these critically endangered snails, researchers from the University of California, Santa Cruz, constructed a reference-quality genome for the species.

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The 1.18 Gb sequence, published May 14 in Journal of Heredity, was assembled using a combination of Pacific Bio HiFi long reads and Omni-C chromatin capture (which crosslinks DNA before sequencing to obtain 3D genomic information). Using a set of reference genes for metazoans, the researchers estimate that the genome is 97.4 percent complete; with a mollusk-specific gene set, it’s estimated to be 86 percent complete.

A black abalone snail with smaller snails behind it
Black abalone were once abundant along the California coast, where their grazing activities played an essential role in the subtidal ecosystem.

The genome adds to the four previous published genomes of other Haliotis species and is the first of a critically endangered abalone, the authors note—indeed, of the NCBI database’s more than 3,200 animal genomes, they point out that only 75 come from mollusks despite Mollusca being the second largest animal phylum.

“The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans,” the team writes in the paper, adding that the sequence should allow scientists to answer key questions about the animals, such as whether there are genomic variations associated with resistance or susceptibility to withering syndrome and whether their population structure indicates ecological barriers to dispersal and settlement that need to be overcome with management actions.

Runners Up:

Balearic Shearwater (Puffinus mauretanicus)

Some estimates suggest that Europe’s most threatened seabird, the Balearic shearwater, will go extinct within the next half century if conservation efforts can’t reverse the steep annual declines in its population. Researchers hope restoration efforts will be aided by a high-quality (estimated 95.9 percent complete) reference genome for the species published May 7 in Genome Biology and Evolution. The team used the sequence to reconstruct the species’ demographic history, which includes a sharp drop in population size roughly 150,000 years ago, coinciding with a period of very low sea levels. “Future ongoing research, using a more powerful population genomics approach, will allow the reconstruction of more recent demographic histories of the species and to test the fossil-based hypotheses of a recent loss of population due to human colonization of the island,” the authors write.

Cultivated oat (Avena sativa)

Cultivated oat has been a staple cereal crop around the world for centuries, thus there has been much interest in developing genomic resources for the species. Unfortunately, the plant’s complex genome contains more than 80,000 genes—far more than humans have—giving geneticists headaches. Finally, though, researchers published a well-annotated, chromosome-scale assembly in Nature on May 18. Analyses utilizing the assembly revealed past large-scale genomic reorganizations that underlie impaired breeding between cultivars. Thanks to the sequence, “[m]odern breeding strategies such as genome editing and gene pyramiding can now more easily be applied in oat to develop varieties that meet the increasing global demand for oat-derived products,” the authors write. In sum, they conclude “this fully annotated hexaploid oat reference genome lays the foundation for advances in oat breeding and basic oat biology and for the ongoing pan-genome project.”  

Genome Spotlight is a monthly column for The Scientist’s Genetics & Genomics newsletter that highlights recently published genome sequences and the mysteries of life they may reveal.