Latest Publications

  • 24 November 2021 • Water Journal


Olena Bilous, Sergey Afanasyev, Olena Lietytska, Oksana Manturova, Oleksandr Polishchuk, Inna Nezbrytska, Maryna Pohorielova andSophia Barinova

  • 16 July 2021 • Pathogens (Special Issue "Genomics, Molecular, Genetics, and Diversity of Plant Disease Resistance")


Sviatoslav Rybnikov, Zeev Frenkel, Abraham B. Korol and Tzion Fahima

Abstract

Antagonistic interactions and co-evolution between a host and its parasite are known to cause oscillations in the population genetic structure of both species (Red Queen dynamics). Potentially, such oscillations may select for increased sex and recombination in the host, although theoretical models suggest that this happens under rather restricted values of selection intensity, epistasis, and other parameters. Here, we explore a model in which the diploid parasite succeeds to infect the diploid host only if their phenotypes at the interaction-mediating loci match. Whenever regular oscillations emerge in this system, we test whether plastic, pathogen-inducible recombination in the host can be favored over the optimal constant recombination. Two forms of the host recombination dependence on the parasite pressure were considered: either proportionally to the risk of infection (prevention strategy) or upon the fact of infection (remediation strategy). We show that both forms of plastic recombination can be favored, although relatively infrequently (up to 11% of all regimes with regular oscillations, and up to 20% of regimes with obligate parasitism). This happens under either strong overall selection and high recombination rate in the host, or weak overall selection and low recombination rate in the host. In the latter case, the system’s dynamics are considerably more complex. The prevention strategy is favored more often than the remediation one. It is noteworthy that plastic recombination can be favored even when any constant recombination is rejected, making plasticity an evolutionary mechanism for the rescue of host recombination.

  • 28 May 2020 • Pathogens (Special Issue "Genomics, Molecular, Genetics, and Diversity of Plant Disease Resistance")


Zhen-Zhen Wei, Valentyna Klymiuk, Valeria Bocharova, Curtis Pozniak and Tzion Fahima

Abstract

The destructive wheat powdery mildew disease is caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt). PmG3M, derived from wild emmer wheat Triticum dicoccoides accession G305-3M, is a major gene providing a wide-spectrum resistance against Bgt. PmG3M was previously mapped to wheat chromosome 6B using an F6 recombinant inbred line (RIL) mapping population generated by crossing G305-3M with the susceptible T. durum wheat cultivar Langdon (LDN). In the current study, we aimed to explore the defense mechanisms conferred by PmG3M against Bgt. Histopathology of fungal development was characterized in artificially inoculated leaves of G305-3M, LDN, and homozygous RILs using fluorescence and light microscopy. G305-3M exhibited H2O2 accumulation typical of a hypersensitive response, which resulted in programmed cell death (PCD) in Bgt-penetrated epidermal cells, while LDN showed well-developed colonies without PCD. In addition, we observed a post-haustorial resistance mechanism that arrested the development of fungal feeding structures and pathogen growth in both G305-3M and resistant RIL, while LDN and a susceptible RIL displayed fully developed digitated haustoria and massive accumulation of fungal biomass. In contrast, both G305-3M and LDN exhibited callose deposition in attempt to prevent fungal invasion, supporting this as a mechanism of a basal defense response not associated with PmG3M resistance mechanism per se. The presented results shed light on the resistance mechanisms conferred by PmG3M against wheat powdery mildew.

  • 13 March 2020 • Pathogens (Special Issue "Genomics, Molecular, Genetics, and Diversity of Plant Disease Resistance")


Yu He, Lihua Feng, Yun Jiang , Lianquan Zhang, Jun Yan, Gang Zhao, Jirui Wang, Guoyue Chen, Bihua Wu, Dengcai Liu, Lin Huang and Tzion Fahima

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat. The wild emmer gene, Yr15 (Wtk1), which confers a strong broad-spectrum resistance to Pst isolates, is composed of kinase and pseudokinase domains. The analysis of 361 wild emmer accessions from a wide range of natural habitats confirms that functional Wtk1 is distributed mainly along a narrow axis from Mt. Carmel to Mt. Hermon regions, in the northern part of Israel, where environmental conditions are favorable to the onset of stripe rust. An analysis of full-length Wtk1 DNA sequences from 49 wild emmer accessions identified three haplotypes and extremely low nucleotide diversity (π = 0.00002). The sequence diversity of Wtk1 is 9.5 times lower than that of broad-spectrum partial resistance gene Yr36 (π = 0.00019), and both are in sharp contrast to the high level of nucleotide diversity previously reported for race-specific resistance genes (e.g., Lr10 and Pm3). However, the nonfunctional wtk1 sequences possess high level of nucleotide diversity (π = 0.07). These results may reflect the different resistance mechanisms and the different evolutionary processes that shaped these resistance genes. Yr15 was absent in 189 Chinese wheat landraces and was present in only 1.02% of the 583 tested modern Chinese wheat cultivars. These results corroborate our previous results showing that Yr15 was absent in 94% of a worldwide collection of 513 wheat cultivars, therefore indicating the importance of Yr15 in wheat stripe rust resistance breeding programs in China and elsewhere around the globe.

  • 29 November 2019 • Pathogens (Special Issue "Genomics, Molecular, Genetics, and Diversity of Plant Disease Resistance")


Moshe Ronen, Hanan Sela, Eyal Fridman, Rafael Perl-Treves, Doris Kopahnke, Alexandre Moreau, Roi Ben-David, and Arye Harel

Abstract

Net blotch (NB) is a major disease of barley caused by the fungus Pyrenophora teres f. teres (Ptt), and P. teres f. maculata (Ptm). Ptt and Ptm infect the cultivated crop (Hordeum vulgare) and its wild relatives (H. vulgare ssp. spontaneum and H. murinum ssp. glaucum). The main goal of this research was to study the NB-causing pathogen in the crop center of origin. To address this, we have constructed a Ptt (n = 15) and Ptm (n = 12) collection isolated from three barley species across Israel. Isolates were characterized genetically and phenotypically. Aggressiveness of the isolates was determined based on necrotrophic growth rate on detached leaves of barley. In addition, isolates were genetically characterized by the mating type, followed by phylogenetic analysis, clustering them into seven groups. The analysis showed no significant differentiation of isolates based on either geographic origin, host of origin or form (Ptt vs. Ptm). Nevertheless, there was a significant difference in aggressiveness among the isolates regardless of host species, geographic location or sampling site. Moreover, it was apparent that the isolates derived from wild hosts were more variable in their necrotrophic growth rate, compared to isolates sampled from cultivated hosts, thereby suggesting that NB plays a major role in epidemiology at the center of barley origin where most of the diversity lies. Ptm has significantly higher necrotrophic and saprotrophic growth rates than Ptt, and for both a significant negative correlation was found between light intensity exposure and growth rates

Abstract

Lake Hula, the core of one of the most extensive wetland complexes in the Eastern Mediterranean, was drained in 1951–1958. However, about 350 hectares of papyrus marshes were allocated in the southwestern part of the previous lake and became the Hula Nature Reserve status, the first of two wetlands in Israel included in the Ramsar List of Wetlands of International Importance. The list of algae and cyanobacteria species of Lake Hula was compiled by us for the first time based on data from publications of 1938–1958, as well as our research in the Hula Nature Reserve, obtained within the framework of the monitoring program for 2007–2013. The list includes 225 species and intraspecies of algae and cyanobacteria belonging to eight phyla. The dynamics of the species richness of algae and cyanobacteria flora for 1938–2013 are shown. Species-bioindicators of water quality have been identified, and the change in their composition by ecological groups for a period of about a hundred years has been shown. Based on the species richness of algae communities, water quality indices were calculated with particular attention to changes in trophic status during the study period. The algae flora of Lake Hula and Hula Nature Reserve was found to be similar, but bioindication has revealed an increase in salinity and organic pollution in recent years

Abstract

We studied the effect of microclimatic gradient on the spatial (8 habitats) and seasonal (autumn, winter, and summer) variations of culturable soil microfungal communities at the north-facing slope (NFS) and the south-facing slope (SFS) of Nahal Boker, the Central Negev Desert, Israel. Using the soil dilution plate method, a total of 122 species from 56 genera was isolated. The communities' composition was subjected to pronounced interslope variations in each season. While xerotolerant melanin-containing species (mainly with the protective multicellular spore morphology) predominated in the soil of NFS, peaking up in the summer, thermotolerant and thermophilic Aspergillus spp. were especially abundant at the SFS. Aspergilli also dominated the thermotolerant communities isolated at 37 °C from both slopes. The more severe microclimatic regime at the SFS resulted in the least pronounced spatial and seasonal intraslope variability of the community composition as compared to the more benign and heterogeneous NFS. The quantitative parameter—the density of microfungal isolates, exhibited significant and positive relationship with organic matter and moisture content. In seasonal dynamics, the severe summer conditions significantly reduced the differences in isolate density at the NFS, which were markedly expressed in the autumn and winter between habitats receiving additional water by runoff and the adjacent habitats that did not benefit from runoff water.

  • 25 October 2021 The Faseb journal


Shaqed Carasso, Bettina Fishman, Liel Stelmach Lask, Tamar Shochat, Naama Geva-Zatorsky, Eran Tauber

Abstract

Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of opposite chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, those factors that shape chronotypes remain poorly understood. Here, we assessed whether the various chronotypes are associated with different gut microbiome compositions. Using metagenomic sequencing analysis, we established a distinct signature associated with chronotype based on two bacterial genera, Alistipes (elevated in “larks”) and Lachnospira (elevated in “owls”). We identified three metabolic pathways associated with the early chronotype, and linked distinct dietary patterns with different chronotypes. Our work demonstrates an association between the gut microbiome and chronotype and may represent the first step towards developing dietary interventions aimed at ameliorating the deleterious health correlates of the late chronotype.

  • 1 September 2021 Molecular Biology and Evolution journal


Kapun, M., Nunez, J.C.B., (and 66 others, including Tauber, E)

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

  • 19 October 2021 Proceedings of the National Academy of Sciences


Quanjun Hu, Yazhen Ma, Terezie Mandáková, Sheng Shi, Chunlin Chen, Pengchuan Sun, Lei Zhang, Landi Feng, Yudan Zheng, Xiaoqin Feng, Wenjie Yang, Jiebei Jiang, Ting Li, Pingping Zhou, Qiushi Yu, Dongshi Wan, Martin A. Lysak, Zhenxiang Xi, Eviatar Nevo, and Jianquan Liu

Abstract

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

  • 07 July 2021 Theoretical and Applied Genetics


Yinghui Li, Zhen-Zhen Wei, Andrii Fatiukha, Samidha Jaiwar, Hanchao Wang, Samiha Hasan, Zhiyong Liu, Hanan Sela, Tamar Krugman & Tzion Fahima

Abstract

Wild emmer wheat (WEW), the tetraploid progenitor of durum and bread wheat, is a valuable genetic resource for resistance to powdery mildew fungal disease caused by Blumeria graminis f. sp. tritici (Bgt). PmG16 gene, derived from WEW, confers high resistance to most tested Bgt isolates. We mapped PmG16 to a 1.4-cM interval between the flanking markers uhw386 and uhw390 on Chromosome 7AL. Based on gene annotation of WEW reference genome Zavitan_V1, 34 predicted genes were identified within the ~ 3.48-Mb target region. Six genes were annotated as associated with disease resistance, of which TRIDC7AG077150.1 was found to be highly similar to Pm60, previously cloned from Triticum urartu, and resides in the same syntenic region. The functional molecular marker (FMM) for Pm60 (M-Pm60-S1) co-segregated with PmG16, suggesting the Pm60 ortholog from WEW (designated here as TdPm60) as a strong candidate for PmG16. Sequence alignment identified only eight SNPs that differentiate between TdPm60 and TuPm60. Furthermore, TdPm60 was found to be present also in the WEW donor lines of the powdery mildew resistance genes MlIW172 and MlIW72, mapped to the same region of Chromosome 7AL as PmG16, suggesting that TdPm60 constitutes a candidate also for these genes. Furthermore, screening of additional 230 WEW accessions with Pm60 specific markers revealed 58 resistant accessions from the Southern Levant that harbored TdPm60, while none of the susceptible accessions showed the presence of this gene. Deployment of PmG16 in Israeli modern bread wheat cultivar Ruta conferred resistance against several local Bgt isolates.

  • 05 May 2021 Plant Biotechnology Journal


Wu Q., Zhao F., Chen Y., Zhang P., Zhang H., Guo G., Xie J., Dong L., Lu P., Li M., Ma S., Fahima T., Nevo E., Li H., Zhang Y., Liu Z.

Abstract

In spite of the obvious climate changes effects on the Carpathian Basin hydrographic nets fish fauna, studies on their potential refuge habitats in drought periods are scarce. Multiannual (2016–2021) research of fish in some streams located in the Saxon Villages area during hydrological drought periods identified, mapped, and revealed the refuge aquatic habitats presence, management needs, and importance for fish diversity and abundance for small rivers. The impact of increasing global temperature and other human activities induced hydrologic net and habitats alteration, decreased the refuge habitats needed by freshwater fish, diminished the fish abundance, and influenced the spatial and temporal variation in fish assemblage structure in the studied area. The sites more than one meter in depth in the studied lotic system were inventoried and all 500 m of these lotic systems were also checked to see what species and how many individuals were present, and if there is was difference in their abundance between refuge and non-refuge 500 m sectors. The scarce number of these refuges due to relatively high soil erosion and clogging in those basins and the cumulative effects of other human types of impact induced a high degree of pressure on the fish fauna. Overall, it reduced the role of these lotic systems as a refuge and for reproduction for the fish of downstream Târnava Mare River, into which all of them flow. Management elements were proposed to maintain and improve these refuges’ ecological support capacity.

Abstract

The evolutionary outcomes of high elevation adaptation have been extensively described. However, whether widely distributed high elevation endemic animals adopt uniform mechanisms during adaptation to different elevational environments remains unknown, especially with respect to extreme high elevation environments. To explore this, we analysed the phenotypic and genomic data of seven populations of plateau zokor (Myospalax baileyi) along elevations ranging from 2,700 to 4,300 m. Based on whole-genome sequencing data and demographic reconstruction of the evolutionary history, we show that two populations of plateau zokor living at elevations exceeding 3,700 m diverged from other populations nearly 10,000 years ago. Further, phenotypic comparisons reveal stress-dependent adaptation, as two populations living at elevations exceeding 3,700 m have elevated ratios of heart mass to body mass relative to other populations, and the highest population (4,300 m) displays alterations in erythrocytes. Correspondingly, genomic analysis of selective sweeps indicates that positive selection might contribute to the observed phenotypic alterations in these two extremely high elevation populations, with the adaptive cardiovascular phenotypes of both populations possibly evolving under the functional constrains of their common ancestral population. Taken together, phenotypic and genomic evidence demonstrates that heterogeneous stressors impact adaptations to extreme elevations and reveals stress-dependent and genetically constrained adaptation to hypoxia, collectively providing new insights into the high elevation adaptation

Abstract

Blind mole rats (BMRs) are small rodents, characterized by an exceptionally long lifespan (>21 years) and resistance to both spontaneous and induced tumorigenesis. Here we report that cancer resistance in the BMR is mediated by retrotransposable elements (RTEs). Cells and tissues of BMRs express very low levels of DNA methyltransferase 1. Following cell hyperplasia, the BMR genome DNA loses methylation, resulting in the activation of RTEs. Upregulated RTEs form cytoplasmic RNA–DNA hybrids, which activate the cGAS–STING pathway to induce cell death. Although this mechanism is enhanced in the BMR, we show that it functions in mice and humans. We propose that RTEs were co-opted to serve as tumor suppressors that monitor cell proliferation and are activated in premalignant cells to trigger cell death via activation of the innate immune response. Activation of RTEs is a double-edged sword, serving as a tumor suppressor but contributing to aging in late life via the induction of sterile inflammation.

  • 1 September 2021 • Nature


Seibold, S., Rammer, W., Hothorn, T., Seidl, R., Ulyshen, M. D., Lorz, J., ..., Pavlíček, T. & Müller, J.

Abstract

The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2,3,4,5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the decomposition of deadwood and carbon release remains poorly understood7. Here we present a field experiment of wood decomposition across 55 forest sites and 6 continents. We find that the deadwood decomposition rates increase with temperature, and the strongest temperature effect is found at high precipitation levels. Precipitation affects the decomposition rates negatively at low temperatures and positively at high temperatures. As a net effect—including the direct consumption by insects and indirect effects through interactions with microorganisms—insects accelerate the decomposition in tropical forests (3.9% median mass loss per year). In temperate and boreal forests, we find weak positive and negative effects with a median mass loss of 0.9 per cent and −0.1 per cent per year, respectively. Furthermore, we apply the experimentally derived decomposition function to a global map of deadwood carbon synthesized from empirical and remote-sensing data, obtaining an estimate of 10.9 ± 3.2 petagram of carbon per year released from deadwood globally, with 93 per cent originating from tropical forests. Globally, the net effect of insects may account for 29 per cent of the carbon flux from deadwood, which suggests a functional importance of insects in the decomposition of deadwood and the carbon cycle.