IMA Genome - F19 : A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras.

The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate. In this issue, we report on a Genome Assembly Workshop for Mycologists that was held at the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa and make available the 12 draft genome sequences emanating from the event. With the aim of making the process of genome assembly and annotation more accessible to biologists, we provide a step-by-step guide to both genome assembly and annotation, intended to encourage and empower mycologists to use genome data in their research.

The Unique Homothallic Mating-Type Loci of the Fungal Tree Pathogens Chrysoporthe syzygiicola and Chrysoporthe zambiensis from Africa.

Chrysoporthe syzygiicola and C. zambiensis are ascomycete tree pathogens first described from Zambia, causing stem canker on Syzygium guineense and Eucalyptus grandis, respectively. The taxonomic descriptions of these two species were based on their anamorphic states, as no sexual states are known. The main purpose of this work was to use whole genome sequences to identify and define the mating-type (MAT1) loci of these two species. The unique MAT1 loci for C. zambiensis and C. syzygiicola consist of the MAT1-1-1, MAT1-1-2, and MAT1-2-1 genes, but the MAT1-1-3 gene is absent. Genes canonically associated with opposite mating types were present at the single mating-type locus, suggesting that C. zambiensis and C. syzygiicola have homothallic mating systems.

Cryphonectriaceae associated with rust-infected Syzygium jambos in Hawaii.

Syzygium jambos (Myrtales, Myrtaceae) trees in Hawaii are severely affected by a rust disease caused by Austropuccinia psidii (Pucciniales, Sphaerophragmiaceae), but they are commonly co-infected with species of Cryphonectriaceae (Diaporthales). In this study, S. jambos and other trees in the Myrtales were examined on three Hawaiian Islands for the presence of Cryphonectriaceae. Bark samples with fruiting bodies were collected from infected trees and fungi were isolated directly from these structures. Pure cultures were produced and the fungi were identified using DNA sequence data for the internal transcribed spacer (ITS) region, part of the ß-tubulin (BT1) gene and the transcription elongation factor-1α (TEF1) gene. Five species in three genera of Cryphonectriaceae were identified from Myrtaceae tree samples. These included Chrysoporthe deuterocubensis, Microthia havanensis and three previously-unknown taxa described here as Celoporthe hauoliensis sp. nov., Cel. hawaiiensis sp. nov. and Cel. paradisiaca sp. nov. Representative isolates of Cel. hauoliensis, Cel. hawaiiensis, Cel. paradisiaca, Chr. deuterocubensis and Mic. havanensis were used in artificial inoculation studies to consider their pathogenicity on S. jambos. Celoporthe hawaiiensis, Cel. paradisiaca and Chr. deuterocubensis produced lesions on young S. jambos trees in inoculation trials, suggesting that, together with A. psidii, they may contribute to the death of trees. Microsatellite markers were subsequently used to consider the diversity of Chr. deuterocubensis on the Islands and thus to gain insights into its possible origin in Hawaii. Isolates of this important Myrtaceae and particularly Eucalyptus pathogen were found to be clonal. This provides evidence that Chr. deuterocubensis was introduced to the Hawaiian Islands as a single introduction, from a currently unknown source.

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed.

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota.

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives.

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defense mechanism that counteracts the deleterious effects of transposable elements. This pathway permanently mutates its target sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence of RIP in the pitch canker pathogen, Fusarium circinatum, and its close relatives in the Fusarium fujikuroi species complex (FFSC). Our results showed that the examined fungi all exhibited hallmarks of RIP, but that they differed in terms of the extent to which their genomes were affected by this pathway. RIP mutations constituted a large proportion of all the FFSC genomes, including both core and dispensable chromosomes, although the latter were generally more extensively affected by RIP. Large RIP-affected genomic regions were also much more gene sparse than the rest of the genome. Our data further showed that RIP-directed sequence diversification increased the variability between homologous regions of related species, and that RIP-affected regions can interfere with homologous recombination during meiosis, thereby contributing to post-mating segregation distortion. Taken together, these findings suggest that RIP can drive the independent divergence of chromosomes, alter chromosome architecture, and contribute to the divergence among F. circinatum and other members of this economically important group of fungi.

The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations.

BACKGROUND: The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. RESULTS: We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. CONCLUSION: This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.

Fungal Systematics and Evolution: FUSE 5.

Thirteen new species are formally described: Cortinarius brunneocarpus from Pakistan, C. lilacinoarmillatus from India, Curvularia khuzestanica on Atriplex lentiformis from Iran, Gloeocantharellus neoechinosporus from China, Laboulbenia bernaliana on species of Apenes, Apristus, and Philophuga (Coleoptera, Carabidae) from Nicaragua and Panama, L. oioveliicola on Oiovelia machadoi (Hemiptera, Veliidae) from Brazil, L. termiticola on Macrotermes subhyalinus (Blattodea, Termitidae) from the DR Congo, Pluteus cutefractus from Slovenia, Rhizoglomus variabile from Peru, Russula phloginea from China, Stagonosporopsis flacciduvarum on Vitis vinifera from Italy, Strobilomyces huangshanensis from China, Uromyces klotzschianus on Rumex dentatus subsp. klotzschianus from Pakistan. The following new records are reported: Alternaria calendulae on Calendula officinalis from India; A. tenuissima on apple and quince fruits from Iran; Candelariella oleaginescens from Turkey; Didymella americana and D. calidophila on Vitis vinifera from Italy; Lasiodiplodia theobromae causing tip blight of Dianella tasmanica 'variegata' from India; Marasmiellus subpruinosus from Madeira, Portugal, new for Macaronesia and Africa; Mycena albidolilacea, M. tenuispinosa, and M. xantholeuca from Russia; Neonectria neomacrospora on Madhuca longifolia from India; Nothophoma quercina on Vitis vinifera from Italy; Plagiosphaera immersa on Urtica dioica from Austria; Rinodina sicula from Turkey; Sphaerosporium lignatile from Wisconsin, USA; and Verrucaria murina from Turkey. Multi-locus analysis of ITS, LSU, rpb1, tef1 sequences revealed that P. immersa, commonly classified within Gnomoniaceae (Diaporthales) or as Sordariomycetes incertae sedis, belongs to Magnaporthaceae (Magnaporthales). Analysis of a six-locus Ascomycota-wide dataset including SSU and LSU sequences of S. lignatile revealed that this species, currently in Ascomycota incertae sedis, belongs to Pyronemataceae (Pezizomycetes, Pezizales).

The mating system of the Eucalyptus canker pathogen Chrysoporthe austroafricana and closely related species.

Fungi in the genus Chrysoporthe are economically important canker pathogens of commercially grown Eucalyptus species and native Myrtales. Before the current study, homothallism was widely accepted as the mating system of these species, but this hypothesis could not be fully tested. Using whole genome sequences, we characterized the MAT locus of two C. austroafricana isolates and its sibling species, C. cubensis and C. deuterocubensis. A unique MAT1-2 idiomorph containing a truncated MAT1-1-1 gene, and a MAT1-1-2 gene, was identified in one isolate of C. austroafricana and a MAT1-1 idiomorph was found in the other. The presence of a single idiomorph in each isolate suggests that this fungus is heterothallic. Screening for MAT genes in 65 C. austroafricana isolates revealed a bias towards MAT1-2 idiomorphs suggesting a recent introduction in Eucalyptus species. Chrysoporthe cubensis and C. deuterocubensis are apparently homothallic since all the expected MAT genes were identified in their genome sequences. These findings were corroborated by the expression profiles of pheromone genes and their receptors, which conformed to the expected patterns observed in heterothallic and homothallic isolates. Long terminal repeat sequences (LTRs) and specifically retrotransposons were identified in the MAT locus of C. deuterocubensis and C. cubensis, indicating that the evolution of mating systems in Chrysoporthe species could be mediated by these elements.

The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure.

Rhipicephalus microplus and R. decoloratus are one-host ticks that preferentially feed on cattle. They are capable of transmitting various tick-borne pathogens which may be detrimental to the agricultural and livestock industry in South Africa. Previous studies have shown that R. microplus forms five lineages in the R. microplus complex, segregating into different geographical areas based on mitochondrial markers. This study examined the phylogenetic relationship within and between R. microplus and R. decoloratus using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The results showed that the nuclear ITS2 marker is informative for interspecific variation but lacks the resolution for intraspecific variation. Analysis of the mitochondrial COI gene revealed that R. microplus ticks from South Africa grouped into a clade comprised of ticks from Asia and South America. The population structure of these two tick species was also investigated using novel microsatellite markers. Population structure analyses revealed that both the R. microplus and R. decoloratus populations presented with two genetic clusters. Rhipicephalus microplus ticks from the Kwa-Zulu Natal (KZN) province belonged to cluster 1, and those from the Eastern Cape (EC) province predominantly grouped into cluster 2. No observable population structure was noted for R. decoloratus. The overlap of genetic clusters in both species could be attributed to inbreeding between the regions by unrestricted movement of cattle across provinces. Such movement promotes tick mobility, gene flow and the homogenisation of tick populations.

Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum.

Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.

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.

Population structure and genetic diversity of Rhipicephalus microplus in Zimbabwe.

Recently there was an expansion in the geographic range of Rhipicephalus microplus in Zimbabwe. In order to understand gene flow patterns and population structure in this highly invasive and adaptable cattle tick, a population genetics study was carried out. Eighty-seven R. microplus tick samples drawn from 5 distinct populations were genotyped using eight polymorphic microsatellite loci. Genetic diversity (He) was high (0.755-0.802) in all the populations, suggesting high levels of gene flow with 97% of genetic variation found within populations and 3% amongst populations. No isolation by distance was observed with low but significant genetic differentiation amongst the populations (0-0.076). Most of the sampled individuals had admixed genetic backgrounds, except for those from Matabeleland North whose genetic makeup appeared different from the rest. Rhipicephalus microplus was recently recorded in this area and the environmental conditions do not support survival of the tick there. These results confirm recent range expansion of the tick and the lowest genetic diversity recorded in the Matabeleland North population is suggestive of a founder effect, which may lead to genetic drift. Generally, the very low levels of genetic differentiation amongst the populations could be a result of the frequent movement of livestock from one area to another, which will have implications for disease control. This study offers further opportunities to study evolutionary adaptation of R. microplus in Zimbabwe and southern Africa.

IMA Genome-F 8: Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips.

The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces. The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.

Evidence for salicylic acid signalling and histological changes in the defence response of Eucalyptus grandis to Chrysoporthe austroafricana.

Eucalyptus species are cultivated for forestry and are of economic importance. The fungal stem canker pathogen Chrysoporthe austroafricana causes disease of varying severity on E. grandis. The Eucalyptus grandis-Chrysoporthe austroafricana interaction has been established as a model system for studying Eucalyptus antifungal defence. Previous studies revealed that the phytohormone salicylic acid (SA) affects the levels of resistance in highly susceptible (ZG14) and moderately resistant (TAG5) clones. The aims of this study were to examine histochemical changes in response to wounding and inoculation as well as host responses at the protein level. The anatomy and histochemical changes induced by wounding and inoculation were similar between the clones, suggesting that anatomical differences do not underlie their different levels of resistance. Tyloses and gum-like substances were present after inoculation and wounding, but cell death occurred only after inoculation. Hyphae of C. austroafricana were observed inside dead and living cells, suggesting that the possibility of a hemibiotrophic interaction requires further investigation. Proteomics analysis revealed the possible involvement of proteins associated with cell death, SA signalling and systemic resistance. In combination with previous information, this study forms a basis for future functional characterisation of candidate genes involved in resistance of E. grandis to C. austroafricana.

Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors.

Chrysoporthe austroafricana is a fungal pathogen that causes the development of stem cankers on susceptible Eucalyptus grandis trees. Clones of E. grandis that are partially resistant and highly susceptible have been identified based on the extent of lesion formation on the stem upon inoculation with C. austroafricana. These interactions have been used as a model pathosystem to enhance our understanding of interactions between pathogenic fungi and woody hosts, which may be different to herbaceous hosts. In previous research, transcriptomics of host responses in these two clones to C. austroafricana suggested roles for salicylic acid and gibberellic acid phytohormone signaling in defense. However, it is unclear how the pathogen infiltrates host tissue and which pathogenicity factors facilitate its spread in the two host genotypes. The aim of this study was to investigate these two aspects of the E. grandis-C. austroafricana interaction and to test the hypothesis that the pathogen possesses mechanisms to modulate the tree phytohormone-mediated defenses. Light microscopy showed that the pathogen occurred in most cell types and structures within infected E. grandis stem tissue. Notably, the fungus appeared to spread through the stem by penetrating cell wall pits. In order to understand the molecular interaction between these organisms and predict putative pathogenicity mechanisms of C. austroafricana, fungal gene expression was studied in vitro and in planta. Fungal genes associated with cell wall degradation, carbohydrate metabolism and phytohormone manipulation were expressed in planta by C. austroafricana. These genes could be involved in fungal spread by facilitating cell wall pit degradation and manipulating phytohormone mediated defense in each host environment, respectively. Specifically, the in planta expression of an ent-kaurene oxidase and salicylate hydroxylase in C. austroafricana suggests putative mechanisms by which the pathogen can modulate the phytohormone-mediated defenses of the host. These mechanisms have been reported in herbaceous plant-pathogen interactions, supporting the notion that these aspects of the interaction are similar in a woody species. This study highlights ent-kaurene oxidase and salicylate hydroxylase as candidates for further functional characterization.

Genetic diversity, acaricide resistance status and evolutionary potential of a Rhipicephalus microplus population from a disease-controlled cattle farming area in South Africa.

The Southern cattle tick, Rhipicephalus microplus is a hematophagous ectoparasite of great veterinary and economic importance. Along with its adaptability, reproductive success and vectoring capacity, R. microplus has been reported to develop resistance to the major chemical classes of acaricides currently in use. In South Africa, the Mnisi community in the Mpumalanga region offers a unique opportunity to study the adaptive potential of R. microplus. The aims of this study therefore included characterising acaricide resistance and determining the level and pattern of genetic diversity for R. microplus in this region from one primary population consisting of 12 communal dip-stations. The level of acaricide resistance was evaluated using single nucleotide polymorphisms (SNPs) in genes that contribute to acaricide insensitivity. Additionally, the ribosomal internal transcribed spacer 2 (ITS2) gene fragments of collected individuals were sequenced and a haplotype network was constructed. A high prevalence of alleles attributed to resistance against formamidines (amitraz) in the octopamine/tyramine (OCT/Tyr) receptor (frequency of 0.55) and pyrethroids in the carboxylesterase (frequency of 0.81) genes were observed. Overall, the sampled tick population was homozygous resistant to pyrethroid-based acaricides in the voltage-gated sodium channel (VGS) gene. A total of 11 haplotypes were identified in the Mnisi R. microplus population from ITS2 analysis with no clear population structure. From these allele frequencies it appears that formamidine resistance in the Mnisi community is on the rise, as the R. microplus populations is acquiring or generating these resistance alleles. Apart from rearing multi-resistant ticks to commonly used acaricides in this community these ticks may pose future problems to its surrounding areas.

IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata.

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.

SNP Analysis Infers that Recombination Is Involved in the Evolution of Amitraz Resistance in Rhipicephalus microplus.

Rhipicephalus microplus, better known as the Asiatic cattle tick, is a largely invasive ectoparasite of great economic importance due to the negative effect it has on agricultural livestock on a global scale, particularly cattle. Tick-borne diseases (babesiosis and anaplasmosis) transmitted by R. microplus are alarming as they decrease the quality of livestock health and production. In sub-Saharan Africa, cattle represent a major source of meat and milk, but this region of the world is severely affected by the Rhipicephalus microplus tick. The principal method for tick control is the use of chemical acaricides, notably amitraz, which was implemented in the 1990's after resistance to other acaricides surfaced. However, the efficiency of chemical control is hindered by an increase in the frequency of mutant resistance alleles to amitraz in tick populations. Presently, the only way to assess amitraz resistance is by means of larval packet tests, but this technique is time-consuming and not particularly cost effective. The main aims of this study were three-fold. First, we attempted to correlate two known SNPs in the octopamine/tyramine (OCT/Tyr) receptor with amitraz resistance in South African field samples of R. microplus. Second, we calculated gametic disequilibrium for these SNPs to determine whether they are randomly associated. Lastly, we conducted a study to assess the evolutionary effects of recombination within the OCT/Tyr receptor. Our results confirmed that the two SNPs are associated with amitraz resistance in the South African tick strain, and that they are in gametic disequilibrium. Additionally, recombination was detected in the OCT/Tyr receptor generating two recombinant haplotypes. These results are of concern to farmers in sub-Saharan Africa, and the emergence of amitraz resistance should be closely monitored in future. Therefore, we present a quick and affordable RFLP based diagnostic technique to assess amitraz resistance in field samples of R. microplus.

IMA Genome-F 5: Draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C. deuterocubensis, Davidsoniella virescens, Fusarium temperatum,Graphilbum fragrans, Penicillium nordicum, and Thielaviopsis musarum.

The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes for the genera Davidsoniella, Graphilbum and Thielaviopsis. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.