Discovery of chloroplast capture in Juniperus excelsa complex by multi- locus phylogeny

Previous studies of nrDNA (nuclear DNA) of Juniperus seravschanica indicated its nuclear DNA (ITS) was from an ancestor of J. polycarpos. However, analysis of cpDNA (chloroplast DNA) suggested the taxon had derived its chloroplast from an ancestor of J. foetidissima. That study has been viewed as putative, because the ITS region is sometimes unreliable for the detection of ancestral hybrids due to concerted evolution and lineage sorting. The recent availability of several single copy nuclear genes (SCNGs) with primers specifically designed for Juniperus presented an opportunity to fully investigate this case of putative chloroplast capture. Three phylogenetic analyses using five SCNGs (LHCA4, maldehy, myb, CnAIP3 and 4CL), ITS region, and four cpDNAs (petN- psbM, trnD-trnT, trnL-trnF and trnS-trnG) were performed on J. seravschanica, as well as other members of the J. excelsa complex: J. excelsa, J. polycarpos, and J. p. var. turcomanica. Analyses revealed incongruence between SCNGs, ITS region and cpDNA showing that J. seravschanica contains an ancestral J. foetidissima/ J. thruifera cp genome. In addition, the phylogenies indicate that the J. excelsa complex is composed of three distinct clades at the species level: J. excelsa, J. polycarpos and J. seravschanica and two varieties of J. polycarpos: J. p. var. polycarpos and J. p. var. turcomanica.

Evidence of inter-sectional chloroplast capture in Corymbia among sections Torellianae and Maculatae

Chloroplast capture through hybridisation and introgression is well described within Eucalyptus. Despite the propensity of the Corymbia genus (eucalypts) to form hybrids from wide crosses, description of chloroplast capture in Corymbia has, until recently, been limited. In this study our aim was to investigate evidence of intersectional chloroplast capture between sections Torellianae and Maculatae. Using whole-genome next-generation sequencing data, the complete chloroplast genomes were assembled from four Corymbia taxa: Corymbia citriodora subspecies citriodora (Hook.) K.D.Hill & L.A.S.Johnson, Corymbia citriodora subspecies variegata (F.Muell.) A.R.Bean & M.W.McDonald, Corymbia henryi (S.T.Blake) K.D.Hill & L.A.S.Johnson, and Corymbia torelliana (F.Muell.) K.D.Hill & L.A.S.Johnson, represented by eight genotypes. Phylogenetic analysis and comparison among Corymbia chloroplast genomes and nuclear external transcribed spacer (ETS) sequences revealed chloroplast capture among Corymbia species across distinct sections Torellianae and Maculatae within subgenus Blakella. Reticulate evolution, along with Eucalyptus, likely extends into Corymbia as evidenced by incongruent plastid and nuclear phylogenetic trees, suggestive of its importance of hybridisation and introgression during the evolution of eucalypts.