Novel de novo genome of Cynopterus brachyotis reveals evolutionarily abrupt shifts in gene family composition across fruit bats.

Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life-history as compared to other bats (e.g. loss of echolocation, large size, frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a previously undiscovered gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle with two other major fruit bat lineages. Most missing genes are regulatory, immune-related and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations, but may often relate to less obvious shifts in immune strategies.