Comparative analysis of bat genomes provides insight into the evolution of flight and immunity

Abstract

Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor κB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.

Fig. 1.. Comparison of bat biological traits

P. alecto and M. davidii represent two distinct Chiropteran suborders and demonstrate diverse evolutionary adaptations. PNG: Papua New Guinea.

Fig 2.. Phylogenomic analysis

Maximum likelihood phylogenomic analysis of 2,492 genes from M. davidii, P. alecto and eight mammalian species. Divergence time estimates in blue, gene family expansion events in green, and gene family contraction events in red. MRCA: most recent common ancestor.

Fig. 3.. Accelerated evolution in the DNA damage checkpoint in bats

(A) Positive selection in the DNA damage checkpoint/DNA repair pathway. Genes under positive selection in the bat ancestor are highlighted in orange. Genes under positive selection in M. davidii only (p53, BRCA2) or P. alecto only (LIG4) are highlighted in blue. (B) Mutations unique to bats were detected in the functionally relevant regions of the p53 nuclear localization signal (NLS) and MDM2 nuclear export signal (NES) (black highlight).