Schuettpelz, Eric , Li, Fay-Wei , Davila, Alexander N. , Cochran, Alyssa .
Streamlining plastid data acquisition in ferns through the use of short, rapidly evolving, coding segments.
Next generation sequencing technologies have greatly reduced both the cost and effort involved in acquiring genomic data. But while such approaches are best suited to obtaining a large number of sequences from a small number of samples, many systematic studies remain better served by incorporating a small number of sequences from a large number of samples. In ferns, targeted sequencing has typically concentrated on either slowly evolving coding regions or rapidly evolving noncoding regions of the plastid genome, depending on the taxonomic level of interest. Unfortunately, both of these marker categories have some well-known limitations. Slowly evolving coding regions (e.g., rbcL or atpA) are broadly alignable but contain relatively little information and are thus inapplicable to lower-level analyses. Rapidly evolving noncoding regions (e.g., trnL-F or trnG-R) are much more variable but are of little use in higher-level analyses where alignment is troublesome. These noncoding regions also tend to incorporate strings of a single nucleotide, which can pose problems for sequencing. Furthermore, most of the regions currently utilized (both coding and noncoding) are too large to be amplified from degraded DNA or sequenced in full with just the amplification primers (additional internal sequencing primers are required). To streamline plastid data acquisition in ferns, we propose a compromise involving the sequencing of short (450 to 750 nucleotide) segments of more rapidly evolving coding regions. This approach reduces sequencing cost and effort while providing data that are useful for both higher-level and lower-level analyses. Here, we provide a thorough comparison of these short, rapidly evolving, coding segments to more commonly sequenced plastid loci, at a variety of taxonomic levels.
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1 - University Of North Carolina Wilmington, Department Of Biology And Marine Biology, 601 South College Road, Wilmington, NC, 28403-5915, USA
2 - DUKE UNIVERSITY, Department Of Biology, BOX 90338, DURHAM, NC, 27708, USA
Presentation Type: Oral Paper:Papers for Sections
Location: Union E/Hyatt
Date: Monday, July 9th, 2012
Time: 1:45 PM