Genomic Biosurveillance Detects A Sexual Hybrid in the Sudden Oak Death Pathogen

Invasive exotic pathogens pose a threat to trees and forest ecosystems worldwide1, hampering the provision of essential ecosystem services such as carbon sequestration and water purification2. Hybridization is a major evolutionary force that can drive the emergence of pathogens3. Phytophthora ramorum, an emergent pathogen that causes the sudden oak and larch death, spreads as reproductively isolated divergent clonal lineages. Sexual recombination has never been reported in this pathogen under natural conditions and laboratory crosses have yielded unfit progenies, suggesting postzygotic barriers to hybridization. Here we report the discovery in a plant nursery of novel variants of P. ramorum that are the result of homoploid hybridization via sexual recombination between North American and European lineages of the pathogen. We show that these hybrids are viable, can infect plants and produce spores for long-term survival and propagation. Genome sequencing revealed novel genotypic combinations, not present in the parental lineages, at 54,515 single nucleotide polymorphism loci. More than 6000 of the novel genotypes at these loci are predicted to have a functional impact in genes associated with host infection, including effectors, carbohydrate-active enzymes and proteases. We also observed post-meiotic mitotic recombination that could generate additional genotypic and phenotypic variation and contribute to homoploid hybrid speciation. Our study highlights the importance of plant pathogen biosurveillance to detect novel variants and inform management and control.

Direct evidence of sex and a hypothesis about meiosis in Symbiodiniaceae

Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts to evolve thermal tolerance in these symbionts and ultimately mitigate coral bleaching, the breakdown of the coral-Symbiodiniaceae partnership under stress. However, direct observations of meiosis in Symbiodiniaceae have not been reported, despite various lines of indirect evidence that it occurs. We present the first cytological evidence of sex in Symbiodiniaceae based on nuclear DNA content and morphology using Image Flow Cytometry, Cell Sorting and Confocal Microscopy. We show the Symbiodiniaceae species, Cladocopium latusorum, undergoes gamete conjugation, zygote formation, and meiosis within a dominant reef-building coral in situ. On average, sex was detected in 1.5% of the cells analyzed (N = 10,000–40,000 cells observed per sample in a total of 20 samples obtained from 3 Pocillopora colonies). We hypothesize that meiosis follows a two-step process described in other dinoflagellates, in which diploid zygotes form dyads during meiosis I, and triads and tetrads as final products of meiosis II. This study sets the stage for investigating environmental triggers of Symbiodiniaceae sexuality and can accelerate the assisted evolution of a key coral symbiont in order to combat reef degradation.

Grape Phylloxera Genetic Structure Reveals Root–Leaf Migration within Commercial Vineyards

Depending on their life cycle, grape phylloxera (Daktulosphaira vitifoliae Fitch) leaf-feeding populations are initiated through asexually produced offspring or sexual recombination. The vine’s initial foliar larvae may originate from root-feeding phylloxera or wind-drifted foliar larvae from other habitats. Though some studies have reported phylloxera leaf-feeding in commercial vineyards, it is still unclear if they are genetically distinct from the population structure of these two sources. Using seven SSR-markers, this study analyzed the genetic structure of phylloxera populations in commercial vineyards with different natural infestation scenarios and that of single-plant insect systems that exclude infestation by wind-drifted larvae. We saw that during the vegetation period, phylloxera populations predominately go through their asexual life cycle to migrate from roots to leaves. We provided evidence that such migrations do not exclusively occur through wind-drifted foliar populations from rootstock vines in abandoned thickets, but that root populations within commercial vineyards also migrate to establish V. vinifera leaf populations. Whereas the former scenario generates foliar populations with high genotypic diversity, the latter produces population bottlenecks through founder effects or phylloxera biotype selection pressure. We finally compared these population structures with those of populations in their native habitat in North America, using four microsatellite markers.

Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents

The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on six continents. The US-1 genotype was found later than FAM-1 on all continents except Australia/Oceania and in only 27% of the samples. FAM-1 was the first genotype detected in almost all the former British colonies from which samples were available. The data from historic outbreak samples suggest the FAM-1 genotype was widespread, diverse, and spread to Asia and Africa from European sources. The famine lineage spread to six continents over 144 years, remained widespread and likely spread during global colonization from Europe. In contrast, modern lineages of P. infestans are rapidly displaced and sexual recombination occurs in some regions.

Clinical malaria incidence following an outbreak in Ecuador was predominantly associated with Plasmodium falciparum with recombinant variant antigen gene repertoires

To better understand the factors underlying the continued incidence of clinical episodes of falciparum malaria in E-2020 countries targeting elimination, we have characterised Plasmodium falciparum disease transmission dynamics after a clonal outbreak on the northwest coast of Ecuador over a period of two years. We apply a novel, high-resolution genotyping method, the "varcode" based on a single PCR to fingerprint the DBLα region of the 40-60 members of the variant surface antigen-encoding var multigene family. Var genes are highly polymorphic within and between genomes, with var repertoires rapidly evolving by outcrossing during the obligatory sexual phase of P. falciparum in the mosquito. The continued incidence of clinical malaria after the outbreak in Ecuador provided a unique opportunity to use varcodes to document parasite microevolution and explore signatures of local disease transmission on the time scale of months to two years post-outbreak. We identified nine genetic varcodes circulating locally with spatiotemporal parasite genetic relatedness networks revealing that diversification of the clonal outbreak parasites by sexual recombination was associated with increased incidence of clinical episodes of malaria. Whether this was due to chance, immune selection or sexual recombination per se is discussed. Comparative analyses to other South American parasite populations where P. falciparum transmission remains endemic elucidated the possible origins of Ecuadorian varcodes. This analysis demonstrated that the majority of clinical cases were due to local transmission and not importation. Nonetheless, some of the varcodes that were unrelated to the outbreak varcode were found to be genetically related to other South American parasites. Our findings demonstrate the utility of the varcode as a high-resolution surveillance tool to spatiotemporally track disease outbreaks using variant surface antigen genes and resolve signatures of recombination in an E-2020 setting nearing elimination.

Direct Evidence Of Sex In Symbiodiniaceae And A Hypothesis About Meiosis

Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts to evolve thermal tolerance in these symbionts and ultimately mitigate coral bleaching, the breakdown of the coral-Symbiodiniaceae partnership under stress. However, direct observations of meiosis in Symbiodiniaceae have not been reported, despite various lines of indirect evidence that it occurs. We present the first cytological evidence of sex in Symbiodiniaceae based on nuclear DNA content and morphology using Image Flow Cytometry, Cell Sorting and Confocal Microscopy. We show Symbiodiniaceae cells undergo gamete conjugation, zygote formation and meiosis within a dominant reef-building coral in situ. On average, sex was detected in 1.5% of the cells analyzed (N=10.000-40.000 cells observed per sample in a total of 20 samples obtained from 3 coral colonies). We show that meiosis follows a two-step process described in other dinoflagellates, in which diploid zygotes form dyads during meiosis I and triads and tetrads as final products of meiosis II. This study sets the stage for investigating environmental triggers of Symbiodiniaceae sexuality and can accelerate the assisted evolution of a key coral symbiont in order to combat reef degradation.

Mixed-Mating Model of Reproduction Revealed in European Phytophthora cactorum by ddRADseq and Effector Gene Sequence Data

A population study of Phytophthora cactorum was performed using ddRADseq sequence variation analysis completed by the analysis of effector genes—RXLR6, RXLR7 and SCR113. The population structure was described by F-statistics, heterozygosity, nucleotide diversity, number of private alleles, number of polymorphic sites, kinship coefficient and structure analysis. The population of P. cactorum in Europe seems to be structured into host-associated groups. The isolates from woody hosts are structured into four groups described previously, while isolates from strawberry form another group. The groups are diverse in effector gene composition and the frequency of outbreeding. When populations from strawberry were analysed, both asexual reproduction and occasional outbreeding confirmed by gene flow among distinct populations were detected. Therefore, distinct P. cactorum populations differ in the level of heterozygosity. The data support the theory of the mixed-mating model for P. cactorum, comprising frequent asexual behaviour and inbreeding alternating with occasional outbreeding. Because P. cactorum is not indigenous to Europe, such variability is probably caused by multiple introductions of different lineages from the area of its original distribution, and the different histories of sexual recombination and host adaptation of particular populations.

Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes

A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study the products of controlled, laboratory-based experiments where known strains or species are crossed in the sand fly vector to generate hybrid progeny. These hybrids can be subsequently studied through high resolution sequencing technologies and software suites such as PAINT that disclose inheritance patterns including ploidies, parental chromosome contributions and recombinations, all of which can inform the sexual strategy. In this work, we discuss the computational methods in PAINT that can be used to interpret the sexual strategies adopted specifically by aneuploid organisms and summarize how PAINT has been applied to the analysis of experimental hybrids to reveal meiosis-like sexual recombination in Leishmania.