Abstract Detail

Phylogenomics

Segovia, Claudia [1], Liston, Aaron [2], Gitzendanner, Matthew [3], Soltis, Douglas [4], Soltis, Pamela [5].

A Phylogenetic Analysis of the Andean Genus Polylepis (Rosaceae) using Next-Generation Sequencing.

The Andean genus Polylepis (Rosaceae) comprises ca. 28 species distributed from Venezuela to northern Argentina occupying high-elevation habitats. These Andean plants have unique ecological and physiological characteristics that allow them to survive in harsh environments such as the Páramo and Puna ecosystems. Polylepis forests play a fundamental role in the hydrological equilibrium of the highlands by protecting water sources. In addition, these forests create refuges for endemic flora and fauna from the high Andes. This uniqueness has attracted the attention of the scientific community in the last decade to understand many aspects of the natural history of Polylepis. However, many areas related to the evolution and systematics of Polylepis remain unclear due to hybridization and polyploidy. Next-Generation Sequencing was employed to understand evolutionary patterns and processes in Polylepis. We sequenced representatives ofof this genus using multiplexed massively parallel sequencing (MMPS) with a combined target enrichment and genome skimming strategy (Hyb-Seq) to obtain sequences of 257 orthologous nuclear loci. The strawberry genome was used as a reference for the design of oligonucleotide RNA baits which were synthesized by MycroArray, Inc. Twenty-six Illumina sequencing libraries were constructed and combined in two multiplex pools. Each pool was used in a single solution hybridization following MycroArray protocols. The 26 libraries were included on one lane of 101-bp, single-end sequencing using an Illumina HiSeq 2000 instrument. A pipeline was designed to scrutinize and assemble the sequence data. Following assembly, sequences were aligned for phylogeny reconstruction, which was carried out using maximum likelihood analyses (ML) with RAxML v. 7.3.1. We describe a method that uses the capacity of next-generation sequence technologies for phylogenetic inference in a group of polyploid plants that seem to have evolved under a recent, rapid radiation.

Broader Impacts:

1 - University of Florida, Florida Museum of Natural History, Dickinson Hall, Gainesville, FL, 32611, USA
2 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA
3 - University of Florida, Florida Museum of Natural History, PO BOX 117800, GAINSVILLE, FL, 32611-7800, USA
4 - University of Florida, Biology/FLMNH, Dickinson Hall , MUseum Road, Gainesville, FL, 32611-7800, USA
5 - University of Florida, Florida Museum of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA

Keywords:
Phylogenomics
Andes
Polylepis
Rosaceae
NGS.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 4:15 PM
Number: 36011
Abstract ID:216
Candidate for Awards:None