Abstract
The Balearic shearwater (Puffinus mauretanicus) is the most
threatened seabird in Europe. The fossil record suggests that human
colonisation of the Balearic Islands resulted in a sharp decrease of the
population size. Currently, populations continue to be decimated mainly
due to predation by introduced mammals and bycatch in longline
fisheries, and some studies predict their extinction by 2070. We present
the first high-quality reference genome for the species which was
obtained by a combination of short and long-read sequencing. Our hybrid
assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a
genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is
amongst the highest across sequenced avian species. This reference
genome allowed us to study critical aspects relevant to the conservation
status of the species, such as an evaluation of overall heterozygosity
levels and the reconstruction of its historical demography. Our
phylogenetic analysis using whole-genome information resolves current
uncertainties in the order Procellariiformes systematics. Comparative
genomics analyses uncover a set of candidate genes that may have played
an important role into the adaptation to a pelagic lifestyle of
Procellariiformes, including those for the enhancement of fishing
capabilities, night vision and the development of natriuresis. This
reference genome will be the keystone for future developments of genetic
tools in conservation efforts for this Critically Endangered species.