Abstract Detail

Phylogenomics

Insupp, Bjorn [1], Erkens, Roy H.J. [2], Brandão, Rita D. [2].

Target enrichment sequencing of the chloroplast genome of  Neotropical Guatteria (Annonaceae) trees.

Guatteria is one of the largest genera of Annonaceae, with c. 180 species. The genus is widely distributed over the Neotropics from the southern region of Mexico to the south of Brazil. It is currently used as a model to understand the evolution of Neotropical forests since it is a common element in these forests. Yet, phylogenetic studies focusing on Guatteria () incorporating information from the whole-chloroplast genome (plastome) have not been conducted, as is true for most other genera. In this study, we have developed home-made baits for target enrichment sequencing of the plastome.
The baits were generated by first designing a series of overlapping primers that tiled the chloroplast genome of previously sequenced Annonaceae from four different genera. The 5-12kb biotinylated-PCR fragments were sheared into about 100bp fragments to function as baits.  A bind and boil assay was performed to check the incorporation of the biotin in the PCR products. Whole Genome DNA from about eighty different Guatteria species was extracted using the modified CTAB DNA extraction method. DNA libraries for the Illumina sequencer were constructed using barcodes that allow multiplexing of 96 samples. An equimolar solution of the sheared biotinylated baits was prepared and mixed with the prepared DNA libraries for hybridization. This method was used to capture the genome of the chloroplast from each Guatteria species in solution. The captured fragments were sequenced using an Illumina MiSeq system aiming for 400x coverage.
Saving cost and time is one of the main advantages of target enrichment with constructed home-made baits. The baits made in this study allow enriching chloroplasts of closely related species. The data generated will be used to infer the species-level biogeographical history of Guatteria  in the Neotropics through phylogenetic analysis.

1 - Maastricht University, Maastricht, the Netherlands
2 - Maastricht University, Maastricht Science Programme, P.O. Box 616, Maastricht, 6200 MD, The Netherlands

Keywords:
Annonaceae
next-generation sequencing
target enrichment
Guatteria.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PPL002
Abstract ID:553
Candidate for Awards:Genetics Section Poster Award