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Abstract Detail


Vargas , Oscar M [1], Simpson, Beryl [1].

Use of genome skimming to resolve phylogenies of recent radiations, a case of a Compositae in the paramo.

In groups where fast diversification has occurred, informative molecular phylogenies are difficult to produce due to low DNA molecular variation. Diplostephium is a genus of ca. 111 species of small trees and sclerophyllous shrubs colloquially known in some places as ‘Paramo Rosemary.’ Close to 60% of the genus’ species inhabit the paramo, while the rest are found in the high Andean mountain forest and puna. Taking into account that paramos are hypothesized to have appeared about 5–2 mya, the high morphological variation in the genus, and the numerous taxa described, it is believed that Diplostephium experienced a recent rapid radiation. Previous molecular data from the internal transcribed spacer and few chloroplast regions has shown that Diplostephium has low molecular divergence between its species. We studied the utility of Next Generation Sequencing (NGS) data to elucidate evolutionary relationships of Diplostephium and its related genera. Genome skimming consists of assembling high-copy genomic fractions of the cell following shallow whole genome sequencing. This technique has the advantage of capturing information from both the uniparentally inherited organellar genomes and the biparentally inherited nuclear DNA. Using 8 million 2x100 pair-end reads sequenced on Illumina 2500 we assembled de-novo the complete chloroplast genome, a part of mitochondrial genome, and the nuclear ribosomal DNA. Our results indicate that the use of genome skimming increased by an order the magnitude the amount of data obtained by average phylogenetic studies using Sanger sequencing. We conclude that genome skimming is a powerful source of phylogenetic information in cases where rapid diversification has occurred.

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Related Links:
Diplostephium website

1 - The University of Texas at Austin, Integrative Biology, 205 W 24th Street, Stop C0930, Austin, TX, 78712, USA

Chloroplast genome
genome skimming
mitochondrial genome
next generation sequencing
rapid radiation
ribosomal DNA.

Presentation Type: Oral Paper:Papers for Topics
Session: 43
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 3:45 PM
Number: 43008
Abstract ID:660
Candidate for Awards:Margaret Menzel Award

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