Yu, Yi , Whetten, Ross , Ranney, Tom , Miller, Ron , Lewandowski, Rick , Xiang, Qiuyun (Jenny) .
Genotyping-by-sequencing for phylogenomics of polyploid species - An experiment with Fothergilla.
Polyploid lineages present major challenges in phylogenetic study due to the extra work required to identify orthologous genes for phylogenetic analyses. Genotyping by sequencing (GBS) provides a powerful tool to rapidly collect large amount of haplotype data on the whole genome scale for population genomics study, and may also hold the potential for elucidating evolutionary relationships among closely related species,especially polyploid taxa. We tested this method using the genus Fothergilla (Hamamelidaceae). Fothergillais a small genus endemic to the Southeastern United States containing two allopatricspecies F. gardenii (4x) in the coastal plains and F. major (6x) onthe upland of the piedmont and mountains. Recent field investigation discovered a few populations of diploid cytotypeshat differ in both morphology and geographic distributions from the polyploidspecies, suggesting that they may represent new, distinct, and rare taxa. The objective of the study is to elucidate the evolutionary relationships of the diploid populations to the previously recognized polyploid taxa using a phylogenomic approach via GBS. In an initial step, we sequenced genomic libraries of 12 accessions prepared by the PstI-GBS method. We took caution to balance the libraries so that multiple alleles and gene copies inpolyploid accessions are equally likely to be detected by the sequencing as those in a diploid accession. After data quality checking and filtering, 16,500 putative loci and 24,337 putative haplotypes were detected using a detection threshold of one nucleotide difference between alleles within a locus and greater than five reads per haplotype per sample. Phylogenetic analysis of data based onhaplotype presence was conducted using the distance method Neighbor-Joining on PAUP*. The results from analyses of different numbers of haplotypes with an increase of 5000 each time consistently recognize the grouping of the five 6xaccessions from F. major. The five 4xaccessions from F. gardenia are separated into two groups. The diploid accession is shown as a distinct lineage more closely related to one of the 4x groups. These relationships are strongly supported by 100 bootstrap values. The distribution of alleles also suggests that the diploid taxon may be the ancestor of the 4x and 6x taxa. These results, while presenting a working hypothesis for testing with more sampling of accessions from each taxon,demonstrate the encouraging potential of genotyping at genomic scale for elucidating evolutionary relationships among closely related polyploid species.
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1 - North Carolina State University, Plant Biology, Department of Plant Biology, Campus Box 7612, Raleigh, North Carolina, 27695, USA
2 - North Carolina State University, Department of Forestry, Raleigh, North Carolina, 27695, United States
3 - North Carolina State University, Department of Horticulture, Raleigh, North Carolina, 27695, United States
4 - University of West Florida , 1157 Ellison Dr., Pensacola, FL, 23503, United States
5 - Mt Cuba Center, Hockessin, DE, 19707, USA
6 - North Carolina State University, Department of Plant Biology, Campus Box 7612, Raleigh, North Carolina, 27695, United States
next generation sequencing
Presentation Type: Oral Paper:Papers for Sections
Location: Delaware D/Hyatt
Date: Wednesday, July 11th, 2012
Time: 11:00 AM