| Abstract Detail
Conference Wide Mandel, Jennifer R [1], Dikow, Rebecca [2], Funk, Vicki [3]. Targeted next-gen sequencing for plant phylogenomics. Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships in plant lineages. In this workshop, we will present an overview of the use of targeted sequence capture and next-generation sequencing for phylogenetics addressing questions like: What do I need to begin a phylogenomics project? How do I design capture probes in my group? What hurdles do I need to be ready for? What kinds of questions can I answer with any existing genomic data I have? How much does this cost? We have successfully implemented targeted capture of low copy sequences followed by next-generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). In this workshop, we will describe the probe design process and the wet lab protocol for performing sequence capture including helpful information for designing similar experiments in your own research system. Our method generates nuclear data and chloroplast genomes (from off-target capture reads) enabling the comparison of nuclear and chloroplast genomes for phylogenetic analyses. We also analyze multi-copy nuclear genes in our data set using a clustering method during orthology detection, and we apply a network approach to these clusters—analyzing all related locus copies. The organizers will demonstrate the bioinformatic and phylogenetic workflow, walk participants through the process, and ample time will be provided for questions at the end. As time allows at the end, materials and software information will be distributed and participants are encouraged to bring their laptops to try out the bioinformatic workflow. Examples will be given for implementing this method in the Compositae and will generalizable to other species groups.
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Related Links:
Mandel Lab
1 - University of Memphis, Department of Biological Sciences, Memphis, TN, 38152, USA
2 - Smithsonian Institute, Smithsonian Institute for Biodiversity Genomics, Washington DC, DC, 20013, USA
3 - Smithsonian Institution, Department of Botany, US National Herbarium, NMNH, MRC166, P.O. Box 37012, Washington DC, DC, 20013-7012, USA, 202-6330950
Keywords:
none specified
Presentation Type: Workshop
Session: WS14, Targeted next-gen sequencing for plant phylogenomics
Location: 104/Savannah International Trade and Convention Center
Date: Sunday, July 31st, 2016
Time: 1:00 PM
Number: WS14001
Abstract ID:33
Candidate for Awards:None |
