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Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

View ORCID ProfileArmin Scheben, View ORCID ProfileOlivia Mendivil Ramos, Melissa Kramer, Sara Goodwin, View ORCID ProfileSara Oppenheim, View ORCID ProfileDaniel J Becker, View ORCID ProfileMichael C Schatz, View ORCID ProfileNancy B Simmons, View ORCID ProfileAdam Siepel, View ORCID ProfileW Richard McCombie
doi: https://doi.org/10.1101/2020.09.09.290502
Armin Scheben
1Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY
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Olivia Mendivil Ramos
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Melissa Kramer
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Sara Goodwin
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Sara Oppenheim
3American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY
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Daniel J Becker
4University of Oklahoma, Department of Biology, Norman, OK
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Michael C Schatz
1Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY
5Johns Hopkins University, Departments of Computer Science and Biology, Baltimore, MD
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Nancy B Simmons
6American Museum of Natural History, Department of Mammalogy, Division of Vertebrate Zoology, New York, NY
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Adam Siepel
1Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY
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  • For correspondence: asiepel@cshl.edu mccombie@cshl.edu
W Richard McCombie
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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  • For correspondence: asiepel@cshl.edu mccombie@cshl.edu
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Abstract

Bats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer. Contiguous and complete reference genomes are needed to determine the genetic basis of these adaptations and establish bats as models for research into mammalian health. Here we sequenced and analysed the genomes of the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus). We sequenced these two species using a mix of Illumina and Oxford Nanopore Technologies (ONT), assembling draft genomes with some of the highest contig N50s (28-29Mb) of bat genomes to date. Work is in progress to increase the base-level accuracies of these genomes. We conducted gene annotation and identified a set of 10,928 orthologs from bats and mammalian outgroups including humans, rodents, horses, pigs, and dogs. To detect positively selected genes as well as lineage-specific gene gains and losses, we carried out comprehensive branch-site likelihood ratio tests and gene family size analyses. Our analysis found signatures of rapid evolution in the innate immune response genes of bats, and evidence of past infections with diverse viral clades in Artibeus jamaicensis and Pteronotus mesoamericanus. We additionally found evidence of positive selection of tumor suppressors, which may play a role in the low cancer rates, in the most recent common ancestor of bats. These new genomic resources enable insights into the extraordinary adaptations of bats, with implications for mammalian evolutionary studies and public health.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus
Armin Scheben, Olivia Mendivil Ramos, Melissa Kramer, Sara Goodwin, Sara Oppenheim, Daniel J Becker, Michael C Schatz, Nancy B Simmons, Adam Siepel, W Richard McCombie
bioRxiv 2020.09.09.290502; doi: https://doi.org/10.1101/2020.09.09.290502
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Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus
Armin Scheben, Olivia Mendivil Ramos, Melissa Kramer, Sara Goodwin, Sara Oppenheim, Daniel J Becker, Michael C Schatz, Nancy B Simmons, Adam Siepel, W Richard McCombie
bioRxiv 2020.09.09.290502; doi: https://doi.org/10.1101/2020.09.09.290502

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