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.

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

and are ascomycete tree pathogens first described from Zambia, causing stem canker on and , 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 () loci of these two species.

The Identification and Characterization of Endopolygalacturonases in a South African Isolate of .

is an economically important plant pathogen that has caused devastating losses to the avocado industry worldwide. To facilitate penetration and successful colonization of the host plant, pathogens have been reported to secrete polygalacturonases (PGs). Although a large PG gene family has been reported in , in-depth bioinformatics analyses and characterization of these genes is still lacking.

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.

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.

Cryphonectriaceae associated with rust-infected in Hawaii.

(Myrtales, Myrtaceae) trees in Hawaii are severely affected by a rust disease caused by (Pucciniales, Sphaerophragmiaceae), but they are commonly co-infected with species of Cryphonectriaceae (Diaporthales). In this study, 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.

Fungal Systematics and Evolution: FUSE 5.

Thirteen new species are formally described: from Pakistan, from India, on from Iran, from China, on species of , , and (Coleoptera, Carabidae) from Nicaragua and Panama, on (Hemiptera, Veliidae) from Brazil, on (Blattodea, Termitidae) from the DR Congo, from Slovenia, from Peru, from China, on from Italy, from , on subsp. from Pakistan. The following new records are reported: on from India; on apple and quince fruits from Iran; from Turkey; and on from Italy; causing tip blight of '' from India; from Madeira, Portugal, new for Macaronesia and Africa; , , and from Russia; on from India; on from Italy; on from Austria; from Turkey; from Wisconsin, USA; and from Turkey.

Repeat-Induced Point Mutations Drive Divergence between 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, , and its close relatives in the species complex (FFSC).

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 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.

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.

Mitochondrial introgression and interspecies recombination in the species complex.

The species complex (FFSC) is an economically important monophyletic lineage in the genus 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.

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

is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many 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 .

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.

IMA Genome-F 8: Draft genome of , , and .

The genomes of , , and are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. and are not known to cause significant disease but are closely related to species of economic importance.

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.

Localization and Transcriptional Responses of in Identify Putative Pathogenicity Factors.

is a fungal pathogen that causes the development of stem cankers on susceptible trees. Clones of that are partially resistant and highly susceptible have been identified based on the extent of lesion formation on the stem upon inoculation with 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 suggested roles for salicylic acid and gibberellic acid phytohormone signaling in defense.

Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species.

In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined.

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.

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.

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.

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.

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.

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.

Evolution of the tissue factor pathway inhibitor-like Kunitz domain-containing protein family in Rhipicephalus microplus.

One of the principle mechanisms utilised by ticks to obtain a blood meal is the subversion of the host's haemostatic response. This is achieved through the secretion of saliva containing anti-haemostatic proteins into the feeding lesion. Lineage-specific expansion of predicted secretory protein families have been observed in all previously studied ticks and occurred in response to adaptation to a blood-feeding environment.