Abstract Detail



Phylogenomics

Amarasinghe, Prabha [1], Jantzen, Johanna [1], Soltis, Douglas [2], SOLTIS, PAMELA S. [3], Cellinese, Nico [2].

Developing tools to capture loci of two distant clades of Melastomataceae.

Next-Generation Sequencing approaches allow understanding of evolutionary relationships using a large number of loci, enabling robust phylogenomic inference in a wide variety of taxa. Although genomes and transcriptomes for focal taxa are popular resources from which to choose target loci, there is a conspicuous literature gap of methodologies to capture loci for taxa with few genomic or transcriptomic resources. Here, we developed a pipeline to target and sequence loci of distantly related Tibouchina and Memecylon clades in Melastomataceae to address evolutionary questions at both fine and broad scales. Transcriptomes of Medinilla magnifica and Tetrazygia biflora from the 1KP database were used as input against reference databases composed of annotated single-copy genes in Arabidopsis thaliana and Theobroma cacao to select loci using the program MarkerMiner. These loci were manually examined to retain genes containing exon sequences longer than 120 bp. The resulting output loci and two trimmed genome skims of Memecylon afzelii and M. toricellense generated from museum specimens were run using HybPiper to obtain the corresponding sequence for the genome skims. Finally, the post-processing scripts in HybPiper were used to retrieve intron regions flanking our targeted exons, and duplicate loci, identified using a reciprocal blast search, were eliminated. Because Memecyon and Tibouchina are distantly related within Melastomataceae, for loci with highly divergent sequences, rather than a consensus sequence of the genome skim and the transcriptome sequences, both sequences were used for probe development. Furthermore, a set of additional genes identified from genomes outside Melastomataceae was targeted for their functional significance. The final set of nuclear loci was used to synthesize a custom bait library. The sequence data generated from this approach will be used to resolve relationships within the Tibouchina and Memecylon clades. Our new pipeline represents a step forward in making maximal use of the information from transcriptomes of distantly related taxa for the investigation of plant evolution at multiple phylogenetic scales.


1 - Florida Museum of Natural History, University of Florida, Department of Biology, University of Florida, 1659 Museum Road, Gainesville, Florida, 32611-7800, United States
2 - Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, Florida, 32611, United States
3 - Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, Florida, 32611, United States

Keywords:
Memecylon
Tibouchina
Melastomataceae
target enrichment
HybPiper.

Presentation Type: Poster
Number: PPH003
Abstract ID:484
Candidate for Awards:None


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