Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

Abstract

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9–10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes.

A dated molecular perspective of eucalypt taxonomy, evolution and diversification

“…Corymbia is classified into subgenera and these could be given genus status. Analyses of nuclear data have suggested that Corymbia subgenera are monophyletic (Schuster et al 2018). In contrast, plastid and concatenated analyses have shown that Corymbia subgenera may not be monophyletic 15 (Schuster et al 2018 and the present study).…”

“…Many of the phylogenies from these studies show a monophyletic Angophora that is sister to a monophyletic Corymbia, with these two genera in turn being sister to a monophyletic Eucalyptus. However, other work, both recent and past, suggests that Angophora could be nested within a paraphyletic Corymbia, with this clade being sister to Eucalyptus (Steane et al 1999;Bayly et al 2013;González-Orozco et al 2016;Schuster et al 2018).…”

“…There are no duplicated specific epithets in the two genera. (3) Another option, if Angophora really is nested within Corymbia, would be to split Corymbia into smaller genera to correct the paraphyly of the latter (Schuster et al 2018).…”

Methods of analysis of Chloroplast Genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

“…Several methods have been used to sequence chloroplast genomes in plants, including primer walking [11][12][13][14] and high-throughput sequencing (HTS) [15]. HTS, both with isolated chloroplast DNA [16][17][18] and total cellular DNA [19][20][21], has been employed to generate physical maps of the chloroplast genome. However, the junctions of LSC/IRa, IRa/SSC, SSC/IRb and IRb/LSC need to be resolved using additional experimentation [22].…”

The complete chloroplast genome sequence of the Australian Mirbelioid peaPlatylobium obtusangulumHook. (Leguminosae: subf. Papilionoideae, tribe Bossiaeeae)

“…Q26846-1; Herbarium voucher specimen: MELUD155101a). Total genomic DNA was isolated from silicadried leaf tissue using a modified CTAB protocol (Shepherd and McLay 2011), prepared for sequencing according to the protocol of Schuster et al (2018), and sequenced on an Illumina NextSeq 550 (mid-output, 2 Â 150 Paired End kit) at The Walter and Eliza Hall Institute of Medical Research (WEHI), Melbourne, Australia. The genome was assembled by mapping contigs built in CLC genomics workbench 10.0.1 using default settings to the reference genome of Indigofera tinctoria (GenBank accession: NC_026680.1) in Geneious 9.1.8 (Kearse et al 2012).…”