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Abstract Detail



Phylogenomics

Qi, Zhechen [1], Yu, Yi [1], Whetten, Ross [2], Ranney, Thomas [3], Miller, Ron [4], Lewandowski, Rick [5], Xiang, Qiuyun (Jenny) [1].

Phylogenomics of Fothergilla by GBS – comparing data yields of experimental repeats and software and evaluating phylogenetic outcomes of taxon sampling and data type.

Fothergilla (Hamamelidaceae) is a small genus endemic to the Southeastern United States. The genus consists of two allopatric polyploidy species and a few diploid populations of unknown taxonomic status. F. gardenii (4x) occurs in the coastal plains and F. major (6x) occurs on the upland of the piedmont and mountains. The diploid populations differ in both morphology and geographic distributions from the polyploid species. The objective of the study is to elucidate the evolutionary relationships of among the diploid populations and polyploid species using data from genotyping by sequencing (GBS). GBS using Illumina Hi-Seq has emerged to be a powerful tool for rapid collection of large amount of haplotype and SNP data on the whole genome scale for population genomics study. We explored the utility of this method in elucidating evolutionary relationships of the diploid populations to the polyploidy species in Fothergilla. We sequenced PstI digested genomic libraries of 51 accessions and compared data yields of different sequencing runs of the same libraries and different software for data processing. We further compare the phylogenetic outcomes of different sampling scales (12 vs 39 accessions) and data types (haplotype versus SNPs). Preliminary results appear to show substantial differences in data yields from different software and in phylogenetic outcomes derived from haplotypes and SNPs.

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1 - North Carolina State University, Department of Plant Biology, Raleigh, NC, 27695-7612, USA
2 - North Carolina State University, Department of Forestry, Raleigh, NC, 27695, USA
3 - North Carolina State University, Department of Horticulture Sciences, Raleigh, North Carolina, 27695
4 - 1157 Ellison Dr., Pensacola, FL, 23503, USA
5 - 5977 Wilson Boulevard, Arlington, VA, 22205, USA

Keywords:
Fothergilla
Phylogenomics
polyploids
next generation sequencing
GBS.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 3:45 PM
Number: 36009
Abstract ID:923
Candidate for Awards:None


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