Dissertation/Thesis Abstract

Phylogenomic Framework of the Plant Family Acanthaceae
by Arias, Joshua Daniel, M.S., California State University, Long Beach, 2019, 95; 13899203
Abstract (Summary)

Acanthaceae is a family of tropical flowering plants with approximately 4000 species, representing morphological, biogeographical, and physiological diversity. Research on patterns of character evolution has been limited by phylogenetic uncertainty along the backbone of the phylogeny. In 2008, McDade et al. estimated a phylogenetic tree of Acanthaceae using four chloroplast loci along with the nuclear ribosomal internal transcribed spacer and relationships among Barlerieae, Andrographideae, Whitfieldieae, and Neuracanthus had low support. I used sequence data from newly sequenced and publicly available transcriptomes and newly sequenced shotgun genome skims to estimate a genome-based phylogeny of the family and to test the chloroplast-based topology. I sampled 16 species of Acanthaceae from the major lineages to estimate a framework of the family phylogeny. I assembled transcriptomes using Trinity and identified coding regions using TransDecoder. I assembled genome skims de novo using SPAdes and predicted coding regions using AUGUSTUS. I combined the predicted coding sequences from transcriptome and shotgun genome skimming in OrthoFinder2 to identify 1,257,148 orthogroups. There were 6,136 loci shared by all 16 species present, allowing for each species to have multiple copies of each locus. OrthoFinder2 was used to infer a species tree from these 6,136 trees that corroborated McDade et al.’s topology, except for the placement of Crabbea. Of the 1,257,148 orthogroups, 587 loci had a single copy for each locus, allowing for some species to have missing data. A RAxML tree based on a multiple sequence alignment of the 587 loci also corroborated McDade et al.’s topology, except for the placement of Crabbea, with high maximum likelihood bootstrap support values. SplitsTree network analyses of the multiple sequence alignment of 587 loci and trees of the 6,136 loci reconciled to the species tree revealed large amounts of conflict among Andrographideae, Whitfieldieae, and Neuracanthus. A principal components analysis in TreeSpace used treeVec, a tree distance metric to identify clusters of trees. There were no distinct clusters in the PCA, suggesting there are no strongly conflicting signals in the nuclear loci that may result from polyploidization or hybridization in the evolutionary history of the family. Of the 587 loci with a single copy for each locus, 10 loci had a single copy with all 16 species present; a RAxML tree estimated from these 10 loci also corroborated McDade et al.’s topology. Our results strongly corroborated the chloroplast-based phylogeny of Acanthaceae with increased resolution among Barlerieae, Andrographideae, Whitfieldieae, and Neuracanthus. The resulting strongly supported tree will now allow us to study character evolution within and between lineages in this diverse group of plants.

Indexing (document details)
Advisor: Fisher, Amanda
Commitee: Brusslan, Judy, Berlemont, Renaud
School: California State University, Long Beach
Department: Biological Sciences
School Location: United States -- California
Source: MAI 81/3(E), Masters Abstracts International
Subjects: Systematic biology, Plant sciences, Bioinformatics
Keywords: Acanthaceae, Phylogeny, Plant evolution, Plant systematics, RNA-seq
Publication Number: 13899203
ISBN: 9781088336748
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