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...
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Online Access: | https://dx.doi.org/10.5061/dryad.s5b40 https://datadryad.org/stash/dataset/doi:10.5061/dryad.s5b40 |
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ftdatacite:10.5061/dryad.s5b40 2024-06-09T07:46:31+00:00 Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... Oomen, Rebekah A. Gillett, Roxanne M. Kyle, Christopher J. 2017 https://dx.doi.org/10.5061/dryad.s5b40 https://datadryad.org/stash/dataset/doi:10.5061/dryad.s5b40 en eng Dryad https://dx.doi.org/10.1111/1755-0998.12027 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 454 sequencing wolverine Gulo gulo multi-locus genes pyrosequencing Major histocompatibility complex Holocene Dataset dataset 2017 ftdatacite https://doi.org/10.5061/dryad.s5b4010.1111/1755-0998.12027 2024-05-13T10:59:08Z 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 ... Dataset Gulo gulo DataCite Metadata Store (German National Library of Science and Technology) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
454 sequencing wolverine Gulo gulo multi-locus genes pyrosequencing Major histocompatibility complex Holocene |
spellingShingle |
454 sequencing wolverine Gulo gulo multi-locus genes pyrosequencing Major histocompatibility complex Holocene Oomen, Rebekah A. Gillett, Roxanne M. Kyle, Christopher J. Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
topic_facet |
454 sequencing wolverine Gulo gulo multi-locus genes pyrosequencing Major histocompatibility complex Holocene |
description |
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 ... |
format |
Dataset |
author |
Oomen, Rebekah A. Gillett, Roxanne M. Kyle, Christopher J. |
author_facet |
Oomen, Rebekah A. Gillett, Roxanne M. Kyle, Christopher J. |
author_sort |
Oomen, Rebekah A. |
title |
Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
title_short |
Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
title_full |
Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
title_fullStr |
Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
title_full_unstemmed |
Data from: Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
title_sort |
data from: comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage ... |
publisher |
Dryad |
publishDate |
2017 |
url |
https://dx.doi.org/10.5061/dryad.s5b40 https://datadryad.org/stash/dataset/doi:10.5061/dryad.s5b40 |
genre |
Gulo gulo |
genre_facet |
Gulo gulo |
op_relation |
https://dx.doi.org/10.1111/1755-0998.12027 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.s5b4010.1111/1755-0998.12027 |
_version_ |
1801376394790305792 |