title: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies.
abstract: Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
authors.affiliation: Department of Biology, Rhodes College, Memphis, TN 38112, USA. Electronic address: andyggardner@gmail.com.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Gardner
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA.
authors.forename: Emily B
authors.initials: EB
authors.lastname: Sessa
authors.affiliation: Department of Biology, Rhodes College, Memphis, TN 38112, USA.
authors.forename: Pryce
authors.initials: P
authors.lastname: Michener
authors.affiliation: Department of Biology, Rhodes College, Memphis, TN 38112, USA.
authors.forename: Eden
authors.initials: E
authors.lastname: Johnson
authors.affiliation: Western Australian Herbarium, Department of Parks and Wildlife, Kensington, WA 6151, Australia.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Shepherd
authors.affiliation: Department of Biological Sciences, St. John's University, Queens, NY 11439, USA.
authors.forename: Dianella G
authors.initials: DG
authors.lastname: Howarth
authors.affiliation: Department of Biology, Rhodes College, Memphis, TN 38112, USA.
authors.forename: Rachel S
authors.initials: RS
authors.lastname: Jabaily
mesh_terms: D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D012270:Ribosomes / Q000235:genetics
keywords: Backbone topology; Goodenia; Goodeniaceae; Nuclear ribosomal repeat; Plastome; Scaevola