Abstract Detail

Phylogenomics

Arias, Joshua [1], McDade, Lucinda [2], Kiel, Carrie [3], Tripp, Erin [4], Fisher, Amanda [5].

Combining Genome Skims and Transcriptomes for a Phylogenomic framework of Acanthaceae.

Acanthaceae is a family of tropical flowering plants with over 4000 species, including Barleria (ca. 300 spp.), Justicia (ca. 400 spp.), and Ruellia (ca. 300 spp.). A 2008 estimate of phylogeny across the family by McDade et al. used four chloroplast loci (trnL-F region, rps16 intron, trnT-L and trnS-G intergenic spacers) and the nuclear ribosomal internal transcribed spacer. Several branches in the resulting tree had low support, particularly relationships between Barlerieae, Andrographideae, Neuracanthus, and Whitfieldieae. To test these relationships we used genome-scale sequence data from 16 species: four publicly available transcriptomes, seven newly sequenced leaf and flower transcriptomes, and five newly sequenced genome skims, to estimate a primarily nuclear phylogeny of the family. We assembled transcriptomes de novo using Trinity and identified coding regions using TransDecoder. Genome skims were assembled de novo using SPAdes and coding regions were predicted in Augustus. Amino acid sequences were used in OrthoFinder2 to identify 1,257,148 orthologous loci. Using several combinations of the data (6,136 orthogroups with all 16 species present, allowing for multiple copies; 587 single-copy loci for at least 9 out of 16 species; 10 single-copy loci with all species present) and several estimation methods (STAG, RAxML, neighbor-net networks, PCAs) we explored phylogenetic signal in the data. A single topology was consistently recovered with high ML bootstrap support. The genome + transcriptome phylogeny corroborates the chloroplast + nrITS estimate, with the exception of the placement of Crabbea. The increased resolution and support for evolutionary relationships in the family will allow us to more confidently infer patterns of character evolution, especially trends in flower color, anther, and pollen morphology. Additionally, the genomic resources resulting from this work will be useful for future studies that increase sampling within each lineage.

1 - California State University, Long Beach, Biological Sciences, 1250 Bellflower Boulevard, Long Beach, CA, 90840, USA
2 - Rancho Santa Botanic Garden, Rancho Santa Ana Botanic Garden, 1500 N College Ave, CLAREMONT, CA, 91711, United States
3 - Rancho Santa Ana Botanic Garden , Botany, 1500 North College Ave., Claremont, CA, 91711, United States
4 - University Of Colorado Museum Herbarium, UCB350, Clare Small Building, Basement, Boulder, CO, 80309, United States
5 - California State University, Long Beach, Biological Sciences, Mail Stop 9502, 1250 Bellflower Blvd, Long Beach, CA, 90840, United States

Keywords:
Lamiales
phylogenomics.

Presentation Type: Oral Paper
Session: PHYL2, Phylogenomics II
Location: Tucson F/Starr Pass
Date: Wednesday, July 31st, 2019
Time: 2:30 PM
Number: PHYL2005
Abstract ID:887
Candidate for Awards:None