Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

Abstract

42 43 ^Joint first authors 44 *joint senior/corresponding authors emails 45 Michael Hiller: hiller@mpi-cbg.de 46 Sonja Vernes: sonja.vernes@mpi.nl 47 Eugene Myers: gene@mpi-cbg.de 48 Emma C. Teeling: emma.teeling@ucd.ie 49 2 Abstract: Bats account for ~20% of all extant mammal species and are considered exceptional 50given their extraordinary adaptations, including biosonar, true flight, extreme longevity, and 51 unparalleled immune systems. To understand these adaptations, we generated reference-quality 52 genomes of six species representing the key divergent lineages. We assembled these genomes 53 with a novel pipeline incorporating state-of-the-art long-read and long-range sequencing and 54 assembly techniques. The genomes were annotated using a maximal evidence approach, de 55 novo predictions, protein/mRNA alignments, Iso-seq long read and RNA-seq short read 56 transcripts, and gene projections from our new TOGA pipeline, retrieving virtually all (>99%) 57 mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 58 conserved non-coding elements identified across 48 mammalian genomes helped to resolve 59 bats' closest extant relatives within Laurasiatheria, supporting a basal position for bats within 60 Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on 61 hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal 62 echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and 63 loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB 64 signalling; and (c) expansion of the APOBEC family, associated with restricting viral infection, 65 transposon activity and interferon signalling. We also identified unique integrated viruses, 66 indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. 67Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory 68 relationships that may contribute to phenotypic diversity in bats. Together, our reference-69 quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed 70 previously unknown genomic adaptations in bats that may explain their extraordinary traits. 71 72

Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats

“…In this study, we report two novel genome assemblies of neotropical fruit bats (the Jamaican fruit‐eating bat, A. jamaicensis , and the yellow‐shouldered bat, S. hondurensis ), which together provide a framework for comparative studies with Old World fruit bats. While we did not generate chromosome‐level genomes such as those of six newly sequenced bat genomes (Jebb et al., 2019), BUSCO assessments showed that our newly sequenced bat genomes are comparable to previously published ones (Table ). Comparative genomics of 10 bat species with diverse diets across the phylogeny revealed a number of convergent genomic signatures of obligate frugivory, including genes involved in sensory perception, digestion and metabolism.…”

“…In this study, we report two novel genome assemblies of neotropical fruit bats (the Jamaican fruit-eating bat, A. jamaicensis, and the newly sequenced bat genomes (Jebb et al, 2019), BUSCO assessments showed that our newly sequenced bat genomes are comparable to previously published ones (Table S4) Because olfactory receptor protein diversity determines the range of molecular ligands that can be recognized (Malnic, Hirono, Sato, & Buck, 1999), OR gene repertoires play a central role in the recognition of volatile organic compounds such as those emitted by ripe fruit. Behavioural studies have shown that olfaction could help bats locate fruits (Kalko & Condon, 1998), and morphological studies show remarkable differences in olfactory bulb size and olfactory epithelium thickness between frugivorous bats and nonfrugivorous bats (Reep & Bhatnagar, 2000), but prior analyses of OR gene repertoires (Hayden et al, 2014) were potentially limited in their OR gene sampling (Yohe et al, 2020).…”

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

“…S5). Relative to other lineages analyzed, Chiroptera has a greater proportion of accelerated versus conserved residues, particularly at the S. However, kidney cell lines derived from dog showed ACE2-dependent SARS-CoV-2 S entry, suggesting that in vitro experiments may be overestimating true infectivity potential (39,50) . Pigs ( low ), ducks ( very low ) and chickens ( very low ) were similarly exposed to SARS-CoV-2 and showed no susceptibility (47) , providing further support of our methodology.…”

“…Phylogenetic analysis of coronaviruses has demonstrated that SARS-CoV-2 most likely originated in a bat species (1 Genomes Project, and other sources (39,40) . We conducted a phylogenetic analysis of ACE2 orthologs from 410 vertebrate species and made predictions of their likelihood to bind the SARS-CoV-2 S using a score that was based on amino acid substitutions at 25 consensus human ACE2 binding residues (13,21) .…”

Novel Insights Into Immune Systems of Bats

“…These studies need to be further validated by an exhaustive search of novel immune-related genes in bats, sampling multiple bat species and sequencing transcripts from different cell types and tissues. The genomes and transcriptomes of at least 18 bat species are currently available in databases (30,41), providing important insights into the evolution of their immune system and antiviral immunity. Below, we discuss the evolution of antiviral responses in bats in the context of cellular detection of RNA and DNA viruses.…”