Preliminary characterization of little brown bats (Myotis lucifugus) immune MHC II DRB alleles using next-generation sequencing
- Published
- Accepted
- Subject Areas
- Bioinformatics, Molecular Biology, Zoology, Immunology
- Keywords
- adaptive immunity, Chiropetera, fungal disease, MHC gene complex, OTU clustering, semiconductor sequencing
- Copyright
- © 2016 Palmer et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Preliminary characterization of little brown bats (Myotis lucifugus) immune MHC II DRB alleles using next-generation sequencing. PeerJ PrePrints 4:e1662v1 https://doi.org/10.7287/peerj.preprints.1662v1
Abstract
Genes of the major histocompatibility complex (MHC) are of great interest to molecular ecologists due to their role in the immune response and the complex evolutionary mechanisms affecting their abundance and distribution. Next generation sequencing (NGS) offers the best potential for characterizing such genes by overcoming the low throughput constraints associated with traditional cloning and Sanger sequencing. However, available bioinformatics methods to effectively filter MHC data acquired through NGS are complex and have not been widely applied. Here we present a method to sequence MHC II DRB of the little brown bat (Myotis lucifugus) using semi-conductor sequencing on the Ion Torrent Personal Genome Machine (PGM) and subsequently analyze the data using a modified UPARSE clustering algorithm. As proof of concept, preliminary characterization of the MHC II DRB alleles of 15 little brown bats was accomplished through PGM sequencing. Analysis identified 24 MHC II DRB alleles overall and a high number of alleles per individual (average 6.8 ± 3.5, range 1 – 12), indicating little brown bats may have among the highest number of MHC DRB loci documented in mammals. Our method provides a framework for studying MHC II DRB diversity in little brown bats, which are experiencing significant population declines in North America due to the recent emergence of white-nose syndrome (WNS).
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Major histocompatibility complex paralogs
Supplementary Figure 1. Multiple DNA sequence alignment of 16 putative MHC II DRB alleles from the reference little brown bat genome, indicating the location of primers and the boundaries of exon 2. The red box indicates where the two forward primers differ.
