Family history identifies sporadic schizoaffective disorder as a subtype for genetic studies

BACKGROUND : Schizophrenia is a heterogeneous disorder with strong genetic vulnerability. Family history of schizophrenia has been considered in genetic studies under several models. De novo genetic events seem to play a larger role in sporadic cases. AIM : This study used the familial–sporadic distinction with the aim of identifying a more homogeneous phenotype to delineate the genetic and clinical complexity of schizophrenia. SETTING : The study was conducted at Weskoppies Hospital, Pretoria, South Africa. METHODS : The study included 384 participants with schizophrenia or schizoaffective disorder from the Afrikaner founder population in South Africa who are considered comparable to Caucasian patients from the United States. A comprehensive data capturing sheet was completed. RESULTS : When schizophrenia and schizoaffective disorder diagnoses were considered jointly, we found no significant differences between the sporadic and the familial groups for age at disease onset, season of birth, comorbid diagnoses, clinical symptomatology, history of suicide or marital status. When the diagnoses were examined separately, however, the sporadic schizoaffective disorder, bipolar type, was found to have a significantly lower age at onset (mean 20.6 vs. 25.3 years). CONCLUSION : The sporadic schizoaffective disorder, bipolar type, forms a more homogeneous subgroup for genetic studies.The National Institute for Mental Health (grant number R01MH61399 to M.K.) and the National Research Foundation (grant number IFR160224159056 to J.L.R).http://www.sajp.org.za/index.php/sajphj2020PsychiatryStatistic

Host switching between native and non-native trees in a population of the canker pathogen Chrysoporthe cubensis from Colombia

The purpose of this study was to test the hypothesis that Chrysoporthe cubensis on native trees in South America could be the source of the pathogen that causes severe stem cankers and often mortality in commercially propagated Eucalyptus trees. This was done by investigating populations originating from two adjacent Eucalyptus (Myrtaceae) plantations in Colombia, and wild Miconia rubiginosa trees (Melastomataceae) growing alongside these stands. Polymorphic microsatellite markers were used to quantify allele sizes in 20 and 39 isolates from the two Eucalyptus stands and 32 isolates from adjacent M. rubiginosa trees. Gene and genotypic diversities were calculated from these data, and population differentiation and assignment tests were performed to ascertain whether the populations were genetically different. Results showed that there were no differences between any of the populations using these techniques, and that they can be treated as a single population. Therefore, the results support the hypothesis that host switching has occurred in C. cubensis in Colombia.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-3059am201

Transmission ratio distortion in an interspecific cross between Fusarium circinatum and Fusarium subglutinans

Previously, an interspecific cross between Fusarium circinatum and Fusarium subglutinans was used to generate a genetic linkage map. A ca. 55 % of genotyped markers displayed transmission ratio distortion (TRD) that demonstrated a genome-wide distribution. The working hypothesis for this study was that TRD would be non-randomly distributed throughout the genetic linkage map. This would indicate the presence of distorting loci. Using a genome-wide threshold of α = 0.01, 79 markers displaying TRD were distributed on all 12 linkage groups (LGs). Eleven putative transmission ratio distortion loci (TRDLs), spanning eight LGs, were identified in regions containing three or more adjacent markers displaying distortion. No epistatic interactions were observed between these TRDLs. Thus, it is uncertain whether the genome-wide TRD was due to linkage between markers and genomic regions causing distortion. The parental origins of markers followed a non-random distribution throughout the linkage map, with LGs containing stretches of markers originating from only one parent. Thus, due to the nature of the interspecific cross, the current hypothesis to explain these observations is that the observed genome-wide segregation was caused by the high level of genomic divergence between the parental isolates. Therefore, homologous chromosomes do not align properly during meiosis, resulting in aberrant transmission of markers. This also explains previous observations of the preferential transmission of F. subglutinans alleles to the F1 progenyThe National Research Foundation (NRF), University of Pretoria, Forestry and Agricultural Biotechnology Institute (FABI), the DST/NRF Center of Excellence in Tree Health Biotechnology (CTHB), members of the Tree Protection Co-operative Programme (TPCP), and the Andrew Mellon Foundation.http://link.springer.com/journal/13258hb201

Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex

The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.The South African National Department of Science and Technology (DST), National Research Foundation (NRF), the Technology and Human Resources of Industry Programme (THRIP) (includes Grant specific unique reference number (UID) 83924), the Tree Protection Cooperative Programme (TPCP), L’Oréal/UNESCO for Women in Science in Sub-Saharan Africa, the Claude Leon Foundation, and the University of Pretoria.http://www.imafungus.orgam2019BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Chrysoporthe puriensis sp. nov. from Tibouchina spp. in Brazil : an emerging threat to Eucalyptus

The discovery of Cryphonectriaceae and more specifically species related to the Eucalyptus canker pathogen Chrysoporthe cubensis on shrubs and trees in the Melastomataceae, has deepened our understanding of relevant, and potentially globally threatening tree pathogens. Recent isolations of Cryphonectriaceae associated with cankers on Tibouchina spp. in Brazil gave rise to an apparently undescribed species of Chrysoporthe associated with stem and branch cankers that lead to tree death. Cultures of this fungus were subjected to phylogenetic studies based on sequences for the ITS and β-tubulin gene regions. These analyses revealed a novel taxon that is described here as Chrysoporthe puriensis sp. nov., having both sexual and asexual states. Pathogenicity tests on two species of Tibouchina (T. granulosa, T. heteromalla) and hybrids of Eucalyptus grandis x E. urophylla showed that Chr. puriensis can infect and cause disease on all of these trees. It is clearly not only damaging on native Tibouchina spp. where environmental conditions are conducive to disease development, but also potentially threatening to non-native Eucalyptus spp., which form the basis of a major plantation forest industry.http://link.springer.com/journal/13313hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Genetic variability in populations of Chrysoporthe cubensis and Chr. puriensis in Brazil

DATA AVAILABILITY STATEMENT: The data that support the findings will be available in NCBI Nucleotide at https://www.re3data.org/search?query=ncbi. The Genbank numbers are given in the text of the manuscript. The data is under embargo until a manuscript is accepted for publication. It will then be openly available.Chrysoporthe puriensis, a sibling species of the well-known Eucalyptus canker pathogen Chr. cubensis, has recently been described from Brazil. Both species are thought to be native to South America, but previous population genetic analyses were conducted prior to the ready availability of robust markers such as microsatellites to test this hypothesis. The objective of this investigation was to analyse the structure and genetic variability of Chr. cubensis and Chr. puriensis populations from non-native Myrtaceae and native Melastomataceae hosts in Brazil, using microsatellite markers developed for this purpose. The fungal isolates were obtained from Eucalyptus species, Corymbia citriodora and Tibouchina species in different regions of the country. Isolates were separated into sub-populations based on host families (Melastomataceae and Myrtaceae) and on region of origin. There was high genetic variability in all sub-populations with the highest levels detected within, rather than among sub-populations. Gene and genotypic diversities were higher for the isolates from the Melastomataceae than the Myrtaceae isolates. High levels of gene flow were found between sub-populations based on host and geographic distribution of the sub-populations. The presence of genetically diverse Chr. cubensis and Chr. puriensis populations on native hosts in Brazil supports a Latin American centre of origin for the two pathogens. Both undergo sexual and asexual reproduction and have a high potential for gene flow.The Tree Protection Co-operative Programme (TPCP) and the DST/NRF Centre of Excellence in Tree Health Biotechnology (South Africa). The FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) for providing scholarships.https://link.springer.com/journal/13313hj2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex

BACKGROUND: The availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called “African”, “Asian” and “American” Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex. RESULTS: Overall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi (“Asian” Clade) is basal in the complex. However, individual mitochondrial gene trees were largely incongruent with one another and with the concatenated gene tree, because six distinct phylogenetic trees were recovered from the various single gene datasets. CONCLUSION: The mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex are remarkably similar to those of the previously characterized Fusarium species and Sordariomycetes. Despite apparently representing a single replicative unit, all of the genes encoded on the mitochondrial genomes of these fungi do not share the same evolutionary history. This incongruence could be due to biased selection on some genes or recombination among mitochondrial genomes. The results thus suggest that the use of individual mitochondrial genes for phylogenetic inference could mask the true relationships between species in this complex.This work is based on the research supported in part by a number of grants from the South African National Department of Science and Technology (DST), National Research Foundation (NRF), Technology and Human Resources of Industry Programme (THRIP) (includes Grant specific unique reference number (UID) 83924).http://www.biomedcentral.com/1471-2164/14/605am201

Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms

The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.National Research Foundation of South Africahttp://www.plosone.orgtm201

First fungal genome sequence from Africa : a preliminary analysis

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.We thank the National Research Foundation (NRF) of South Africa, members of the Tree Protection Co-operative Programme, the THRIP initiative of the Department of Trade and Industry and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology and the Oppenheimer Foundation for funding.http://www.sajs.co.zanf201

Fungal Planet description sheets : 320–370

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana malaysiana from Acacia mangium. Furthermore, Stachybotrys sansevieriicola is described from Sansevieria ehrenbergii (Tanzania), Phacidium grevilleae from Grevillea robusta (Uganda), Graphium jumulu from Adansonia gregorii and Ophiostoma eucalyptigena from Eucalyptus marginata (Australia), Pleurophoma ossicola from bone and Plectosphaerella populi from Populus nigra (Germany), Colletotrichum neosansevieriae from Sansevieria trifasciata, Elsinoë othonnae from Othonna quinquedentata and Zeloasperisporium cliviae (Zeloasperisporiaceae fam. nov.) from Clivia sp. (South Africa), Neodevriesia pakbiae, Phaeophleospora hymenocallidis and Phaeophleospora hymenocallidicola on leaves of a fern (Thailand), Melanconium elaeidicola from Elaeis guineensis (Indonesia), Hormonema viticola from Vitis vinifera (Canary Islands), Chlorophyllum pseudoglobossum from a grassland (India), Triadelphia disseminata from an immunocompromised patient (Saudi Arabia), Colletotrichum abscissum from Citrus (Brazil), Polyschema sclerotigenum and Phialemonium limoniforme from human patients (USA), Cadophora vitícola from Vitis vinifera (Spain), Entoloma flavovelutinum and Bolbitius aurantiorugosus from soil (Vietnam), Rhizopogon granuloflavus from soil (Cape Verde Islands), Tulasnella eremophila from Euphorbia officinarum subsp. echinus (Morocco), Verrucostoma martinicensis from Danaea elliptica (French West Indies), Metschnikowia colchici from Colchicum autumnale (Bulgaria), Thelebolus microcarpus from soil (Argentina) and Ceratocystis adelpha from Theobroma cacao (Ecuador). Myrmecridium iridis (Myrmecridiales ord. nov., Myrmecridiaceae fam. nov.) is also described from Iris sp. (The Netherlands). Novel genera include (Ascomycetes): Budhanggurabania from Cynodon dactylon (Australia), Soloacrosporiella, Xenocamarosporium, Neostrelitziana and Castanediella from Acacia mangium and Sabahriopsis from Eucalyptus brassiana (Malaysia), Readerielliopsis from basidiomata of Fuscoporia wahlbergii (French Guyana), Neoplatysporoides from Aloe ferox (Tanzania), Wojnowiciella, Chrysofolia and Neoeriomycopsis from Eucalyptus (Colombia), Neophaeomoniella from Eucalyptus globulus (USA), Pseudophaeomoniella from Olea europaea (Italy), Paraphaeomoniella from Encephalartos altensteinii, Aequabiliella, Celerioriella and Minutiella from Prunus (South Africa). Tephrocybella (Basidiomycetes) represents a novel genus from wood (Italy). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.Alina V. Alexandrova was supported by the Russian Science Foundation (project N 14-50-00029). Ekaterina F. Malysheva, Olga V. Morozova, Alexander E. Kovalenko and Eugene S. Popov acknowledge financial support from the Russian Foundation for Basic Research (project 13-04-00838a and 15-04-04645a). Margarita Dueñas, María P. Martín and M. Teresa Telleria acknowledge financial support from the Plan Nacional I+D+I projects No. CGL2009-07231 and CGL2012-3559. Cony Decock gratefully acknowledges the financial support received from the FNRS / FRFC (convention FRFC 2.4544.10), the CNRS-French Guiana and the Nouragues staff, which enabled fieldwork in French Guiana, and the Belgian State – Belgian Federal Science Policy through the BCCMTM research programme.http://www.ingentaconnect.com/content/nhn/pimjam201