Show simple item record Sanders, Sheri Papudeshi, Bhavya Ganote, Carrie Doak, Tom Mansfield, Charles Tseng, Chi Yen Custer, Thomas Custer, Christine Matson, Cole 2019-01-16T20:06:27Z 2019-01-16T20:06:27Z 2019-01-14
dc.identifier.citation S. Sanders, C. Mansfield, B. Papudeshi, C. Ganote, C.Y. Tseng, T. Custer, C. Custer, C. Matson, T. Doak. 2019. Population Genetics of Tree Swallows, in Collaboration with NCGAS. Plant and Animal Genomes XXVII, San Diego, CA. Retrieved from en
dc.description.abstract The National Center for Genome Analysis Support (NCGAS) provides training and computational resources in an effort to train biologists to approach historically-difficult, non-model problems with large biological data sets. For example, our collaborators at Baylor University work with Tree Swallow (Tachycineta bicolor), using RNAseq data in population genetics and toxicology. Working with the NCGAS, they assembled a de novo transcriptome assembly for the Tree Swallow, for which there is no genome. Variant calling using the transcriptome identified 66,169 single nucleotide polymorphisms (SNPs) across 144 samples. They were then able to identify phylogeographic structuring across the Great Lakes Region, including accurate grouping populations distributed across smaller geographic scales (e.g. along the Maumee River). SNPs were also used to assess population heterozygosity and genetic diversity. This project required large scale data handling, large memory machines to assembly the transcriptome, and advanced Linux skills to manage the data and analyses. NCGAS provided the computation resources and training on the Linux environment and data management. Further assistance was provided in consultation and problem solving - leading to a high level of independence and competency of the graduate student researcher. en
dc.description.sponsorship This research is based upon work supported by the National Science Foundation under grant No. ABI-1759906 to Indiana University. en
dc.language.iso en en
dc.publisher Plant and Animal Genome XXVII en
dc.rights Except where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This license includes the following terms: You are free to share -to copy, distribute and transmit the work and to remix -to adapt the work under the following conditions: attribution -you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work. en
dc.rights.uri en
dc.subject NCGAS en
dc.subject transcriptome assembly en
dc.subject population genetics en
dc.subject exotoxicology en
dc.title Population Genetics of Tree Swallows, in Collaboration with NCGAS en
dc.type Presentation en

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