Abstract Detail


Gomez, Jorge [1], Moore, Erika [2], Burke, John [3], Mandel, Jennifer [4].

A tale of two Hyb-Seq probe sets: Comparing the Compositae-1061 probe set with a new probe set targeting 2424 functional genes.

The sunflower family, Asteraceae, comprises 10% of all flowering plant species on Earth and displays an incredible diversity of form. Asteraceae are clearly monophyletic yet resolving phylogenetic relationships within the family has historically proven difficult, thus hindering our ability to understand its origin and diversification. However, over the past 10 years, the Compositae-1061 probe set, which targets 1,061 conserved orthologs, has been used to resolve relationships both along the backbone of the family and at lower taxonomic levels within several genera. As a part of efforts to study potentially adaptive genes in the sunflower family, we developed a new probe set, hereafter referred to as ‘Aster-2424’, that targets 2,424 candidate functional genes from Helianthus annuus transcriptomic sequence. As a first step toward understanding how well this new probe set enriches for loci across the family, we have carried out Hyb-Seq methods on 16 taxa that have also been analyzed previously with the Compositae-1061 probe set. Briefly, Illumina-style genomic libraries were prepared using the NEBNext Ultra protocol and sequence capture was carried out using a custom set of myBaits from Daicel Arbor Biosciences that targets transcription factors, hormone pathway and biosynthesis genes, and a set of curated candidate genes mined from the literature. High-throughput sequencing was performed on an Illumina HiSeq instrument. The resulting data from the new probe set were analyzed using the HybPiper pipeline to assign orthology across loci, then analyzed in the ASTRAL framework. The resulting Aster-2424 probe set phylogeny is compared to the reconstructed phylogeny from the Compositae-1061 probe set, along with statistics for each of the recovered loci. Future work will also investigate evidence for natural selection on genes from the new probe set using molecular evolutionary analyses.

Related Links:
Mandel Lab Website

1 - University of Memphis, Biological Sciences, 3700 Walker Ave, Memphis, TN, 38152, USA
2 - University Of Memphis, Biological Sciences, 3700 Walker Ave, 322 Ellington Hall, Memphis, TN, 38152, United States
3 - University Of Georgia, Dept Of Plant Biology, Miller Plant Sciences, Athens, GA, 30602, United States
4 - University Of Memphis, Biological Sciences, 3700 Walker Ave, 339 Ellington Hall, Memphis, TN, 38152, United States

candidate genes
probe sets.

Presentation Type: Poster
Number: PPL010
Abstract ID:828
Candidate for Awards:None

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