Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ...
Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time-intensive and indirect methods of asses...
| Main Authors: | , , |
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| Format: | Dataset |
| Language: | English |
| Published: |
Dryad
2017
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.s5b40 https://datadryad.org/stash/dataset/doi:10.5061/dryad.s5b40 |
| Summary: | Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time-intensive and indirect methods of assessment often underestimate total variation. Here, we explored the suitability of 454 pyrosequencing for characterizing multilocus genes for use in population genetic studies. We compared two sample tagging protocols and two bioinformatic procedures for 454 sequencing through characterization of a 185-bp fragment of MHC DRB exon 2 in wolverines (Gulo gulo) and further compared the results with those from cloning and Sanger sequencing. We found 10 putative DRB alleles in the 88 individuals screened with between two and four alleles per individual, suggesting amplification of a duplicated DRB gene. In addition to the putative alleles, all individuals possessed an easily identifiable pseudogene. In our system, sequence ... : Reads from run 163 of Gulo gulo MHC DRB exon 2 fragmentReads from run 245 of Gulo gulo MHC DRB exon 2 fragmentReads from run 329-1 of Gulo gulo MHC DRB exon 2 fragmentReads from run 329-2 of Gulo gulo MHC DRB exon 2 fragmentReads from run 329-3 of Gulo gulo MHC DRB exon 2 fragmentReads from run 329-4 of Gulo gulo MHC DRB exon 2 fragmentReads from run Trent-1 of Gulo gulo MHC DRB exon 2 fragmentList of individuals and MID tags for Gulo gulo MHC DRB exon 2 sequencing reads ... |
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