Abstract Detail

Phylogenomics

Amarasinghe, Prabha [1], Jantzen, Johanna [1], Folk, Ryan [2], Soltis, Douglas [2], Soltis, Pamela [2], Cellinese, Nico [2].

Developing a new bioinformatics pipeline to capture low-copy nuclear loci for two distant clades of Melastomataceae.

High-coverage genomes and especially transcriptomes, in the clades where they are available, are popular resources from which to develop target loci for phylogenomic inferences in plants. Such well-curated resources do not cover many clades; genome-skimming data are more broadly distributed across taxa, but current methodologies cannot use such data for locus development. Melastomataceae is an example of a large clade with few genomic resources available. Here, we used a two-tier approach to develop low-copy nuclear loci for the distantly related Memecylon and Tibouchina clades in Melastomataceae, and to build an RNA bait set to address evolutionary questions at both fine and broad scales. In the first tier, we used MarkerMiner to compare the transcriptomes of Tetrazygia bicolor and Medinilla magnifica from the 1KP project to the genomes of Arabidopsis thaliana and Theobroma cacao to select putatively single-copy loci. In the second tier, the resulting output loci from MarkerMiner and two trimmed genome skims of Memecylon and Tibouchina were run through HybPiper to retrieve assemblies for the selected loci from genome-skimming data. The post-processing scripts in HybPiper were used to retrieve intron regions flanking our targeted exons, and a reciprocal blast search was used to screen for and remove multi-copy loci. We also developed a set of non-single-copy loci with functional significance and added previously published single-copy nuclear loci. To test our 384 loci (which were covered by 11,871 probes), we hybridized libraries from 91 Memecylon samples and 144 samples of Tibouchina, examining success at both deep and shallow evolutionary levels. For each clade, we conducted phylogenomic analyses using RAxML (concatenation) and ASTRAL (coalescence) to estimate the species trees. We found that the novel low-copy nuclear loci from this pipeline are effective for both Memecylon and Tibouchina at multiple phylogenetic scales.

1 - Florida Museum of Natural History, Department of Biology, University of Florida, 1659 Museum Rd, Gainesville, Florida, 32611, USA
2 - Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, Florida, 32611, USA

Keywords:
Memecylon
Tibouchina
Melastomataceae
phylogenomics
target enrichment
MarkerMiner
HybPiper.

Presentation Type: Poster
Session: P, Phylogenomics Posters
Location: Arizona Ballroom/Starr Pass
Date: Monday, July 29th, 2019
Time: 5:30 PM This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PPL008
Abstract ID:595
Candidate for Awards:None