Phytophthora ramorum

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests (Rizzo et al. 2002, 2005). This oomycete pathogen was discovered in Marin County, California, in the mid-1990s, causing sudden oak death on coast live oak (Quercus agrifolia) and tanoak (Notholithocarpus densiflorus) and simultaneously discovered in Europe causing foliar blight on Rhododendron and Viburnum (Rizzo et al. 2002; Werres et al. 2001). It is now known to affect more than 100 plant species, including economically important nursery and forest host species (Frankel 2008; Rizzo et al. 2005; Tooley et al. 2004; Tooley and Kyde 2007)

Historia evolutiva del grupo previamente denominado protistas usando una aproximación filogenómica

La falta de organización en linajes discretos en la filogenia y la taxonomía del grupo anteriormente llamado protistas ha retrasado la comprensión de la historia evolutiva del grupo y la comparación de rasgos entre los miembros del mismo. En este estudio usamos una aproximación filogenómica para plantear hipótesis filogenéticas del grupo mencionado. Usamos una estrategia basada en el agrupamiento automático de ortólogos (OrthoMCL) para recuperar 72 grupos de ortólogos de 73 especies. Un árbol obtenido con el método de maxima verosimilitud fue estimado a partir de una supermatriz de datos. De manera general obtuvimos inferencias filogenéticas consistentes con publicaciones previas pero se observaron algunos patrones de ramificación inesperados con valores bajos de soporte. A pesar de la gran cantidad de genes de los grupos Opisthokonta, este clado aparece polifilético. No pudimos demostrar la monofilia de Excavata, muy probablemente debido a artefactos de atracción de ramas largas. Un segundo conjunto de datos fue construido luego de eliminar los sitios de rápida evolución/saturados. El test de Shimodaira-Hasegawa se calculó con el fin de verificar si nuestros datos e inferencias filogenéticas controvertían patrones de ramificación reportados previamente. Los resultados de los tests sugieren que las topologías propuestas en estudios previos no son significativamente mejores que las topologías propuestas en este estudio. Nuevas relaciones fueron encontradas dentro de los Opisthokonta, para dos especies, Thecamonas trahens y Capsaspora owczarzaki. Adicionalmente, algunas posiciones filogenéticas controversiales se encontraron para varios grupos eucariotas con nuestra aproximación filogenómica. En el estudio se discuten las relaciones de los grupos Alveolata y Stramenopila, siendo este ultimo grupo de especial interés para nuestro grupo de investigación.The lack of organisation of monophyletic lineages in the phylogeny and taxonomy of the group formerly known as protists has precluded the understanding of the group's evolutionary history and trait comparison among members of the group. We used a phylogenomic approach to establish phylogenetic hypotheses of this group of organisms. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences with previous published ones, but some unexpected phylogenetic relationships were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade was recovered as polyphyletic. We failed to recover a monophyletic Excavata group, most likely because of long- branch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject relationships in previous hypotheses. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two species, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found. We discuss the relative positions of the Alveolata and Stramenopila groups, the latter being of special interest in our research group

Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010

Synechococcus spp. are unicellular cyanobacteria widely distributed in the world\u27s oceans. We report the complete genome sequence of Synechococcus sp. strain NB0720_010, isolated from Narragansett Bay, Rhode Island. NB0702_10 has several large (.3,000-amino acid) protein-coding genes that may be important in its interactions with other cells, including grazers in estuarine habitats

Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus . Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.Keywords: Clone correction, Microbiology, Genotypic diversity, Genetics, Bootstrap, Computational Science, Bioinformatics, Population genetics, Hierarchy, Mycology, Clonality, Permutation, Minimum spanning networks, Index of association, Bruvo’s distanceThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/

The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics

The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility.

BACKGROUND: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. RESULTS: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. CONCLUSION: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas

Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto)

In the Amazon the only described species of Cordyceps sensu stricto (Hypocreales, Cordycipitaceae) that parasitize insects of Orthopterida (orders Orthoptera and Phasmida) are Cordyceps locustiphila and C. uleana. However, the type specimens for both taxa have been lost and the concepts of these species are uncertain. To achieve a more comprehensive understanding of the systematics of these species, collections of Cordyceps from the Amazon regions of Colombia, Ecuador and Guyana were subjected to morphological, ecological and molecular phylogenetic studies. Phylogenetic analyses were conducted on partial sequences of SSU, LSU, TEF, RPB1 and RPB2 nuclear loci. Two new species are proposed including C. diapheromeriphila, a parasite of Phasmida, and C. acridophila, a parasite of the superfamily Acridomorpha (Orthoptera), which is broadly distributed across the Amazon. For C. locustiphila a lectotypification and an epitypification are made. Cordyceps locustiphila is host specific with Colpolopha (Acridomorpha: Romaleidae), and its distribution coincides with that of its host. The phylogenetic placement of these three species was resolved with strong support in the Beauveria clade of Cordyceps s. str. (Cordycipitaceae). This relationship and the morphological similarity of their yellow stromata with known teleomorphs of the clade, suggest that the holomorphs of these species may include Beauveria or Beauveria-like anamorphs. The varying host specificity of the beauverioid Cordyceps species suggest the potential importance of identifying the natural host taxon before future consideration of strains for use in biological control of pest locusts.This is the publisher’s final pdf. The article is copyrighted by the Mycological Society of America and published by Allen Press Inc. It can be found at: http://www.mycologia.org/.Keywords: Host specificity, Anamorph-teleomorph connection, Entomopathogenic fungi, Phylogeny, Orthoptera, Neotropic

Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races

The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, “red core”. The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens

Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR