New chromosome number records of South African Oxalis species

Chromosome numbers of only 49 Oxalis L. taxa have been published to date, of which just 23 represent southern African taxa. Chromosome counts for the follOW ing southern African taxa are recorded here for the first time: O. bifida Thunb., O. hirta L. var. tubiflora Salter and O. semiloba Sond A third record for O. truncatula Jacq is also presented here Two previous counts for th is species have been published, one revealing a tetraploid and the other a hexaploid condition. All four taxa Included here have a basic chromosome number of x = 7, O. bifida and O. truncatula are both diploid, whereas O. hirta var. tubiflora and O. semiloba were both found to be tetraploid. The diploid form of O. truneatula found here completes a polyploid series (2x, 4x and 6x) in this species. It is concluded that karyological data can greaUy aid our understanding of the massive diversification and speciation of Oxalis in southern Africa Further cytological studies are recommende

Section Reniformia, a new section in the genus Pelargonium (Geraniaceae)

A new section of Pelargonium L’Héerit. (Geraniaceae), section Reniformia (Knuth) Dreyer is described in which 8 species and 2 subspecies are included. Pelargonium reniforme Curt, is designated as the type species for the section. All included species are endemic to southern Africa, with the majority of taxa centred in the Eastern Cape Province Section Reniformia is characterised by its floral structure, a basic chromosome number of x = 8 and pollen grains with a striate-reticulale tectum

Genetic basis for high population diversity in Protea-associated Knoxdaviesia

Sexual reproduction is necessary to generate genetic diversity and, in ascomycete fungi, this process is controlled by a mating type (MAT) locus with two complementary idiomorphs. Knoxdaviesia capensis and K. proteae (Sordariomycetes; Microascales; Gondwanamycetaceae) are host-specific saprophytic fungi that show high population diversity within their Protea plant hosts in the Cape Floristic Region of South Africa. We hypothesise that this diversity is the result of outcrossing driven by a heterothallic mating system and sought to describe the MAT1 loci of both species. The available genome assembly of each isolate contained only one of the MAT1 idiomorphs necessary for sexual reproduction, implying that both species are heterothallic. Idiomorph segregation during meiosis, a 1:1 ratio of idiomorphs in natural populations and mating experiments also supported heterothallism as a sexual strategy. Long-range PCR and shot-gun sequencing to identify the opposite idiomorph in each species revealed no sequence similarity between MAT1-1 and MAT1-2 idiomorphs, but the homologous idiomorphs between the species were almost identical. The MAT1-1 idiomorph contained the characteristic MAT1-1-1 and MAT1-1-2 genes, whereas the MAT1-2 idiomorph consisted of the genes MAT1-2-7 and MAT1-2-1. This gene content was similar to that of the three species in the Ceratocystidaceae (Microascales) with characterized MAT loci. The Knoxdaviesia MAT1-2-7 protein contained and alpha domain and predicted intron, which suggests that this gene arose from MAT1-1-1 during a recombination event. In contrast to the Ceratocystidaceae species, Knoxdaviesia conformed to the ancestral Sordariomycete arrangement of flanking genes and is, therefore, a closer reflection of the structure of this locus in the Microascalean ancestor.The National Research Foundation (NRF) and the Department of Science and Technology (DST)-NRF Centre of Excellence in Tree Health Biotechnology (CTHB).http://www.elsevier.com/locate/yfgbi2017-11-30hb2017GeneticsMicrobiology and Plant Patholog

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb‐Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA cistron from 23 southern African Oxalis species. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb‐Seq in phylogenetics

Multi-gene phylogeny for Ophiostoma spp. reveals two new species from Protea infructescences

Ophiostoma represents a genus of fungi that are mostly arthropod-dispersed and have a wide global distribution. The best known of these fungi are carried by scolytine bark beetles that infest trees, but an interesting guild of Ophiostoma spp. occurs in the infructescences of Protea spp. native to South Africa. Phylogenetic relationships between Ophiostoma spp. from Protea infructescences were studied using DNA sequence data from the β-tubulin, 5.8S ITS (including the flanking internal transcribed spacers 1 and 2) and the large subunit DNA regions. Two new species, O. phasma sp. nov. and O. palmiculminatum sp. nov. are described and compared with other Ophiostoma spp. occurring in the same niche. Results of this study have raised the number of Ophiostoma species from the infructescences of serotinous Protea spp. in South Africa to five. Molecular data also suggest that adaptation to the Protea infructescence niche by Ophiostoma spp. has occurred independently more than once

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

n Taksonomiese studie van Pelargonium seksie Cortusina (Geraniaceae)

Proefskrif (M. Sc.) -- Universiteit van Stellenbosch, 1990.Full text to be digitised and attached to bibliographic record

Genomic overview of closely related fungi with different Protea host ranges

Genome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche.Supplementary File 1: Summary of repeat-induced-point mutation (RIP) per scaffold.Supplementary File 2: Examples of the sequence depth and number of mismatches across repetitive regions in Knoxdaviesia capensis and K. proteae.Supplementary File 3: Overview of the classification of Knoxdaviesia genome-wide speciesspecific proteins in Functional Catalogue categories.Supplementary File 4: Classification and annotation of the genome-wide species-specific proteins of Knoxdaviesia capensis and K. proteae.Supplementary File 5: Knoxdaviesia species-specific proteins putatively involved in secondary metabolism.Supplementary File 6: Summary of proteins excluded from and included in the final secretome dataset.Supplementary File 7: Overview of the classification of Knoxdaviesia secreted proteins in Functional Catalogue categories.Supplementary File 8: Classification and annotation of the putative secreted proteins of Knoxdaviesia capensis and K. proteae.Supplementary File 9: Classification and annotation of the small secreted cysteine-rich proteins (SSCPs) identified in the two Knoxdaviesia genomes.Supplementary Table S1: Occurrence of the TTAGGGTTAC / GTAACCCTAA Knoxdaviesia telomere repeat in K. capensis and K. proteae. Supplementary Table S2: Populous orthogroups in the Knoxdaviesia genomes. Supplementary Table S3: Outcome of the protein BLAST for the Knoxdaviesia capensis and K. proteae species-specific proteins. Supplementary Table S4: Cysteine-rich secreted proteins and proteins with hits to the Pathogen Host Interaction (PHI) database in Knoxdaviesia capensis and K. proteae. Supplementary Table S5: Amplification of the T1PKS-4 cluster deletion in Knoxdaviesia capensis and K. proteae.Supplementary Data: The predicted proteins of Knoxdaviesia capensis and K. proteae in FASTA format and the gff3 annotation files of the transposable elements identified by the REPET package have been made available on Mendeley Data (https://data.mendeley.com/), DOI:10.17632/rbx32w7crp.1The National Research Foundation (NRF) and the Department of Science and Technology (DST) - NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and the SARChI chair in Fungal Genomics.http://www.elsevier.com/locate/funbio2019-12-01hj2018BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog