Recent Topics Posters
Hansen, Kimberly , Straub, Shannon , Liston, Aaron .
Efficient Plastome Assembly from Next-Generation Sequencing Data.
The ever increasing sequencing capacity of Illumina's sequencing by synthesis technology presents the potential to transform the field of plant systematics, so long as systematists are not deterred by what may seem like overwhelming amounts of data. Plant plastid genomes (plastomes) present an opportunity for new users of this technology to develop skills in genomic analyses due to their tractable size, and conserved gene content and organization.Using the Alignreads pipeline ( Straub et al. 2011 BMC Genomics 12:211), we assembled full plastomes of over 200 Aclepias sp. and closely related Apocynaceae generated from total genomic DNA as well as more than 150 gymnosperms generated from DNA amplicons. We discuss the limitations of reference guided assembly using single end, short reads including repetitive regions, inversions, gene rearrangements, polynucleotides and more. Our focus is to present the post pipeline manual editing steps necessary to identify and edit any resulting misassembly.This discussion is intended to encourage systematists to incorporate this powerful technology into their research.
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1 - 411 W. Aspen, Flagstaff, AZ, 86001, USA
2 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
3 - Oregon State University, Department of Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
Presentation Type: Recent Topics Poster
Location: Battelle South/Convention Center
Date: Monday, July 9th, 2012
Time: 5:30 PM