De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability

Abstract

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.