14 April 2025 • Nature Genetics
Wheat tandem kinase RWT4 directly binds a fungal effector to activate defense
Yi-Chang Sung, Yinghui Li, Zoe Bernasconi, Suji Baik, Soichiro Asuke, Beat Keller, Tzion Fahima & Gitta Coaker
Plants have intricate innate immune receptors that detect pathogens. Research has intensely focused on two receptor classes recognizing external and internal threats. Recent research has identified a class of disease-resistance proteins called tandem kinase proteins (TKPs). We investigated RWT4, a wheat TKP that confers resistance to the devastating fungal pathogen Magnaporthe oryzae. We established a rice protoplast system, revealing RWT4 specifically recognizes the AvrPWT4 effector, leading to the transcription of defense genes and inducing cell death. RWT4 possesses both kinase and pseudokinase domains, with its kinase activity essential for defense. RWT4 directly interacts with and transphosphorylates AvrPWT4. Biolayer interferometry revealed both RWT4 kinase and pseudokinase regions bind the effector. Sequence similarity and structural modeling revealed a partial kinase duplication in RWT4’s kinase region as critical for effector interaction and defense activation. Collectively, these findings demonstrate that TKPs can directly bind a recognized effector, leading to downstream defense activation.
30 January 2025 • Plant Cell Environment
Nikolai Govta, Liubov Govta, Hanan Sela, Gadi Peleg, Assaf Distelfeld, Tzion Fahima, Diane M. Beckles, Tamar Krugman
Our aim was to elucidate mechanisms underlying nitrogen (N)-deficiency tolerance in bread wheat (cultivar Ruta), conferred by a wild emmer wheat QTL (WEW; IL99). We hypothesised that the tolerance in IL99 is driven by enhanced N-uptake through modification of root system architecture (RSA) underscored by transcriptome modifications. Severe N-deficiency (0.1 N for 26 days) triggered significantly higher plasticity in IL99 compared to Ruta by modifying 16 RSA traits; nine of which were IL99-specific. The change in root growth in IL99 was collectively characterised by a transition in root orientation from shallow to steep, increased root number and length, and denser networks, enabling nutrient acquisition from a larger volume and deeper soil layers. Gene ontology and KEGG-enrichment analyses highlighted IL99-specific pathways and candidate genes elevated under N-deficiency. This included Jasmonic acid metabolism, a key hormone mediating RSA plasticity (AOS1, TIFY, MTB2, MYC2), and lignification-mediated root strengthening (CYP73A, 4CL). ‘N-metabolism’ was identified as a main shared pathway to IL99 and Ruta, with enhanced nitrate uptake predominant in IL99 (NRT2.4), while remobilisation was the main strategy in Ruta (NRT2.3). These findings provide novel insights into wheat plasticity response underlying tolerance to N-deficiency and demonstrate the potential of WEW for improving N-uptake under suboptimal conditions.
30 January 2025 • Nature Communications
Frédéric Jiguet, Asaf Mayrose, Markus Piha, Ron Efrat, Tuomas Seimola, Nir Sapir, Sami Timonen, Yohay Wasserlauf, Aurélien Besnard, Pierrick Bocher, Andrea Kölzsch, Aleksi Lehikoinen, Anne-Christine Monnet, Petr Procházka & Yoav Perlman
In war and conflict zones, the jamming of Global Navigation Satellite System (GNNS) signals by military forces disrupts the tracking of tagged animals, and has increased in frequency following the recent escalation of conflicts in Eastern Europe and the Middle East. Such disruption to data collection strongly hampers research into the protection and conservation of endangered animals.
20 February 2025 • Journal of Fungi
Jie Fang, Mihal Blaschkauer, Assaf Distelfeld, Zihao Liu, Bin Song, Shimon Rachmilevitch andJonathan M. Adams
While the differences between domesticated crops and their wild relatives have been extensively studied, less is known about their rhizosphere microbiomes, which hold potential for breeding stress-resistant traits. We compared the rhizosphere microbiomes of domesticated wheat (Triticum aestivum L.) and its wild ancestor (Triticum turgidum ssp. dicoccoides) in a typical agricultural field using 16S rRNA and ITS gene sequencing. Our results revealed a high level of conservation in the rhizosphere microbiomes between wild and domesticated wheat, with minimal divergence in community composition and microbial network structure. However, domesticated wheat exhibited a higher prevalence of fungal pathogens and increased functional redundancy, with significant enrichment of genes involved in carbon and nitrogen cycling. The microbial community assemblies in both wheats were predominantly governed by deterministic processes. This suggests that long-term conventional agricultural practices have imposed minor effects on the compositional differences between the microbiomes of wild and domesticated wheat. Nonetheless, the lower abundance of apparent pathogens in the rhizosphere of the wild wheat suggests greater natural biota or innate host plant resistance against pathogenic fungi. This study may provide valuable insights into the host selection, assembly patterns, and functional potential of microbial communities in wild versus domesticated wheat, with implications for manipulating microbial communities in future crop breeding
06 March 2025 • npj Aging
Gesa Poetzsch, Luca Jelacic, Leon Dammer, Sören Lukas Hellmann, Michelle Balling, Miguel Andrade-Navarro, Aaron Avivi, Imad Shams, Anne Bicker & Thomas Hankeln
In the subterranean rodent (Nanno)spalax galili, evolutionary adaptation to hypoxia is correlated with longevity and tumor resistance. Adapted gene-regulatory networks of Spalax might pinpoint strategies to maintain health in humans. Comparing liver, kidney and spleen transcriptome data from Spalax and rat at hypoxia and normoxia, we identified differentially expressed gene pathways common to multiple organs in both species. Body-wide interspecies differences affected processes like cell death, antioxidant defense, DNA repair, energy metabolism, immune response and angiogenesis, which may play a crucial role in Spalax’s adaptation to environmental hypoxia. In all organs, transcription of genes for genome stability maintenance and DNA repair was elevated in Spalax versus rat, accompanied by lower expression of aerobic energy metabolism and proinflammatory genes. These transcriptomic changes might account for the extraordinary lifespan of Spalax and its cancer resistance. The identified gene networks present candidates for further investigating the molecular basis underlying the complex Spalax phenotype.
02 December 2024 • Nature Plants
Regulation and function of a polarly localized lignin barrier in the exodermis
Concepcion Manzano, Kevin W. Morimoto, Lidor Shaar-Moshe, G. Alex Mason, Alex Cantó-Pastor, Mona Gouran, Damien De Bellis, Robertas Ursache, Kaisa Kajala, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, J. Carlos del Pozo & Siobhan M. Brady
Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli.
08 January 2025 • Nature Genetics
Tandem kinase proteins across the plant kingdom
Tamara Reveguk, Andrii Fatiukha, Evgenii Potapenko, Ivan Reveguk, Hanan Sela, Valentyna Klymiuk, Yinghui Li, Curtis Pozniak, Thomas Wicker, Gitta Coaker & Tzion Fahima
Plant pathogens pose a continuous threat to global food production. Recent discoveries in plant immunity research unveiled a unique protein family characterized by an unusual resistance protein structure that combines two kinase domains. This study demonstrates the widespread occurrence of tandem kinase proteins (TKPs) across the plant kingdom. An examination of 104 plant species’ genomes uncovered 2,682 TKPs. The majority (95.6%) of these kinase domains are part of the receptor-like kinase–Pelle family, which is crucial for cell surface responses in plant immunity. Notably, 90% of TKPs comprise dual kinase domains, with over 50% being pseudokinases. Over 56% of these proteins harbor 127 different integrated domains, and over 47% include a transmembrane domain. TKP pseudokinases and/or integrated domains probably serve as decoys, engaging with pathogen effectors to trigger plant immunity. The TKP Atlas we created sheds light on the mechanisms of TKP convergent molecular evolution and potential function.
01 September 2024 • Molecular Ecology
36-year study reveals stability of a wild wheat population across microhabitats
Tal Dahan-Meir, Thomas James Ellis, Fabrizio Mafessoni, Hanan Sela, Ori Rudich, Jacob Manisterski, Naomi Avivi-Ragolsky, Amir Raz, Moshe Feldman, Yehoshua Anikster, Magnus Nordborg, Avraham A. Levy
Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.
15 November 2024 • Nature Communications
A single NLR gene confers resistance to leaf and stripe rust in wheat
Davinder Sharma, Raz Avni, Juan Gutierrez-Gonzalez, Rakesh Kumar, Hanan Sela, Manas Ranjan Prusty, Arava Shatil-Cohen, István Molnár, Kateřina Holušová, Mahmoud Said, Jaroslav Doležel, Eitan Millet, Sofia Khazan-Kost, Udi Landau, Gerit Bethke, Or Sharon, Smadar Ezrati, Moshe Ronen, Oxana Maatuk, Tamar Eilam, Jacob Manisterski, Pnina Ben-Yehuda, Yehoshua Anikster, Oadi Matny, …Amir Sharon
Nucleotide-binding leucine-rich repeat (NLR) disease resistance genes typically confer resistance against races of a single pathogen. Here, we report that Yr87/Lr85, an NLR gene from Aegilops sharonensis and Aegilops longissima, confers resistance against both P. striiformis tritici (Pst) and Puccinia triticina (Pt) that cause stripe and leaf rust, respectively. Yr87/Lr85 confers resistance against Pst and Pt in wheat introgression as well as transgenic lines. Comparative analysis of Yr87/Lr85 and the cloned Triticeae NLR disease resistance genes shows that Yr87/Lr85 contains two distinct LRR domains and that the gene is only found in Ae. sharonensis and Ae. longissima. Allele mining and phylogenetic analysis indicate multiple events of Yr87/Lr85 gene flow between the two species and presence/absence variation explaining the majority of resistance to wheat leaf rust in both species. The confinement of Yr87/Lr85 to Ae. sharonensis and Ae. longissima and the resistance in wheat against Pst and Pt highlight the potential of these species as valuable sources of disease resistance genes for wheat improvement.
02 January 2024 • Nature Plants
A suberized exodermis is required for tomato drought tolerance
Alex Cantó-Pastor, Kaisa Kajala, Lidor Shaar-Moshe, Concepción Manzano, Prakash Timilsena, Damien De Bellis, Sharon Gray, Julia Holbein, He Yang, Sana Mohammad, Niba Nirmal, Kiran Suresh, Robertas Ursache, G. Alex Mason, Mona Gouran, Donnelly A. West, Alexander T. Borowsky, Kenneth A. Shackel, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, Song Li, Rochus Benni Franke & Siobhan M. Brady
Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.
27 September 2023 • Nature Communications
Social isolation shortens lifespan through oxidative stress in ants
Akiko Koto, Makoto Tamura, Pui Shan Wong, Sachiyo Aburatani, Eyal Privman, Céline Stoffel, Alessandro Crespi, Sean Keane McKenzie, Christine La Mendola, Tomas Kay & Laurent Keller
Social isolation negatively affects health, induces detrimental behaviors, and shortens lifespan in social species. Little is known about the mechanisms underpinning these effects because model species are typically short-lived and non-social. Using colonies of the carpenter ant Camponotus fellah, we show that social isolation induces hyperactivity, alters space-use, and reduces lifespan via changes in the expression of genes with key roles in oxidation-reduction and an associated accumulation of reactive oxygen species. These physiological effects are localized to the fat body and oenocytes, which perform liver-like functions in insects. We use pharmacological manipulations to demonstrate that the oxidation-reduction pathway causally underpins the detrimental effects of social isolation on behavior and lifespan. These findings have important implications for our understanding of how social isolation affects behavior and lifespan in general.
17 July 2024 • Theoretical and Applied Genetics
Nikolai Govta, Andrii Fatiukha, Liubov Govta, Curtis Pozniak, Assaf Distelfeld, Tzion Fahima, Diane M Beckles, Tamar Krugman
Genetic dissection of a QTL from wild emmer wheat, QGpc.huj.uh-5B.2, introgressed into bread wheat, identified candidate genes associated with tolerance to nitrogen deficiency, and potentially useful for improving nitrogen-use efficiency. Nitrogen (N) is an important macronutrient critical to wheat growth and development; its deficiency is one of the main factors causing reductions in grain yield and quality. N availability is significantly affected by drought or flooding, that are dependent on additional factors including soil type or duration and severity of stress. In a previous study, we identified a high grain protein content QTL (QGpc.huj.uh-5B.2) derived from the 5B chromosome of wild emmer wheat, that showed a higher proportion of explained variation under water-stress conditions. We hypothesized that this QTL is associated with tolerance to N deficiency as a possible mechanism underlying the higher effect under stress. To validate this hypothesis, we introgressed the QTL into the elite bread wheat var. Ruta, and showed that under N-deficient field conditions the introgression IL99 had a 33% increase in GPC (p < 0.05) compared to the recipient parent. Furthermore, evaluation of IL99 response to severe N deficiency (10% N) for 14 days, applied using a semi-hydroponic system under controlled conditions, confirmed its tolerance to N deficiency. Fine-mapping of the QTL resulted in 26 homozygous near-isogenic lines (BC4F5) segregating to N-deficiency tolerance. The QTL was delimited from - 28.28 to - 1.29 Mb and included 13 candidate genes, most associated with N-stress response, N transport, and abiotic stress responses. These genes may improve N-use efficiency under severely N-deficient environments. Our study demonstrates the importance of WEW as a source of novel candidate genes for sustainable improvement in tolerance to N deficiency in wheat.
10 April 2024 • Nature Communications
Miaomiao Li, Huaizhi Zhang, Huixin Xiao, Keyu Zhu, Wenqi Shi, Dong Zhang, Yong Wang, Lijun Yang, Qiuhong Wu, Jingzhong Xie, Yongxing Chen, Dan Qiu, Guanghao Guo, Ping Lu, Beibei Li, Lei Dong, Wenling Li, Xuejia Cui, Lingchuan Li, Xiubin Tian, Chengguo Yuan, Yiwen Li, Dazhao Yu, Eviatar Nevo, Tzion Fahima, Hongjie Li, Lingli Dong, Yusheng Zhao & Zhiyong Liu
Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance.
18 April 2024 • Journal of Molecular Evolution
Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads
Leo Douglas Creasey & Eran Tauber
Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to DNA damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in DNA methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.
15 February 2024 • ACS Omega
Francesco Coppola, Tomáš Pavlíček and Petr Král
The COVID-19 infection has been more problematic for individuals with certain health predispositions. Coronaviruses could also interfere with neural diseases if the viruses succeed in entering the brain. Therefore, it might be of principal interest to examine a possible coupling of coronaviruses and amyloid fibrils. Here, molecular dynamics simulations were used to investigate direct coupling of SARS-CoV-2 and Aβ fibrils, which play a central role in neural diseases. The simulations revealed several stable binding configurations and their dynamics of Aβ42 fibrils attached to spike proteins of the Omicron and Alpha variants of SARS-CoV-2.
09 January 2024 • nature ecology & evolution
Xuan An, Leyan Mao, Yinjia Wang, Qinqin Xu, Xi Liu, Shangzhe Zhang, Zhenglei Qiao, Bowen Li, Fang Li, Zhuoran Kuang, Na Wan, Xiaolong Liang, Qijiao Duan, Zhilong Feng, Xiaojie Yang, Sanyuan Liu, Eviatar Nevo, Jianquan Liu, Jay F. Storz & Kexin Li
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai–Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.
5 December 2023 • Nature Communications
Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle
Yang Zhao, Zhizhong Zheng, Zhihui Zhang, Yandong Xu, Eric Hillpot, Yifei S. Lin, Frances T. Zakusilo, J. Yuyang Lu, Julia Ablaeva, Seyed Ali Biashad, Richard A. Miller, Eviatar Nevo, Andrei Seluanov & Vera Gorbunova
Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species’ cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle.
22 October 2023 • Journal of Fungi
Maxim Krakhmalnyi, Omoanghe S. Isikhuemhen, Mikael Jeppson, Solomon P. Wasser, Eviatar Nevo
The diversity of Lycoperdaceae in Israel was studied. Molecular phylogenetic relationships within the family, and genus Lycoperdon in particular, were inferred using original ITS rDNA sequences of 58 samples belonging to 25 species from Israel and six other countries, together with 66 sequences stored in the GenBank database. The current molecular phylogenetic study recovered the family Lycoperdaceae as a monophyletic group, which was supported in both maximum likelihood and Bayesian analyses. The clades corresponding to the genera Apioperdon, Bovista, Calvatia, Disciseda, and Lycoperdon were revealed. The taxonomic structure of the named genera was partially resolved. Within the genus Lycoperdon, some species received significant statistical support; however, their relationships, as well as the problem of the genus monophyly, mostly remained questionable. As a result of a thorough literature survey, extensive sample collection, and studies of the material stored in the Herbarium of the Institute of Evolution, University of Haifa (HAI, Israel), fifteen species representing five genera were found in the territory of Israel. Six species, namely Apioperdon pyriforme, Bovista aestivalis, Calvatia candida, Lycoperdon decipiens, L. niveum, and L. perlatum, are new additions to the diversity of Lycoperdaceae in Israel. Detailed macro- and micromorphological descriptions, ecology, geography, and critical notes, together with light microscopy photos and SEM micrographs, are provided. In-depth discussion on some taxonomically challenging species is presented.
6 July 2023 • Plant Communications
Yinghui Li , Zhen-Zhen Wei , Hanan Sela, Liubov Govta, Valentyna Klymiuk, Rajib Roychowdhury, Harmeet Singh Chawla, Jennifer Ens, Krystalee Wiebe, Valeria Bocharova, Roi Ben-David, Prerna B. Pawar, Yuqi Zhang, Samidha Jaiwar, István Molnár, Jaroslav Doležel, Gitta Coaker 8, Curtis J. Pozniak, Tzion Fahima
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.
14 June 2023 • Biology
Loren Khatib, Bengisu Sezen Subasi, Bettina Fishman, Martin Kapun, and Eran Tauber
Our understanding of the gene regulatory network that constitutes the circadian clock has greatly increased in recent decades, notably due to the use of Drosophila as a model system. In contrast, the analysis of natural genetic variation that enables the robust function of the clock under a broad range of environments has developed more slowly. In the current study, we analyzed comprehensive genome sequencing data from wild European populations of Drosophila, which were densely sampled through time and space. We identified hundreds of single nucleotide polymorphisms (SNPs) in nine genes associated with the clock, 276 of which exhibited a latitudinal cline in their allele frequencies. While the effect sizes of these clinal patterns were small, indicating subtle adaptations driven by natural selection, they provided important insights into the genetic dynamics of circadian rhythms in natural populations. We selected nine SNPs in different genes and assessed their impact on circadian and seasonal phenotypes by reconstructing outbred populations fixed for either of the SNP alleles, from inbred DGRP strains. The circadian free-running period of the locomotor activity rhythm was affected by an SNP in doubletime (dbt) and eyes absent (Eya). The SNPs in Clock (Clk), Shaggy (Sgg), period (per), and timeless (tim) affected the acrophase. The alleles of the SNP in Eya conferred different levels of diapause and the chill coma recovery response.
22 May 2023 • Nature genetics
Tzion Fahima & Gitta Coaker
Two studies describe kinase fusion proteins (KFPs) that regulate the perception and deception of wheat pathogens. These highlight the emergence of KFPs as plant immune regulators and emphasize the importance of crop wild relatives as a reservoir for resistance breeding and global food security.
17 April 2023 • PNAS
Pnina Cohen, Roberto Bacilieri, Jazmín Ramos-Madrigal, Eyal Privman, Elisabetta Boaretto, Audrey Weber, Daniel Fuks, Ehud Weiss, Tali Erickson-Gini, Scott Bucking, Yotam Tepper, Deborah Cvikel, Joshua Schmidt, M. Thomas P. Gilbert, Nathan Wales, Guy Bar-Oz and Meirav Meir
Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780–19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.
1 February 2023 • Nature Communications
Gilad Gabay, Hanchao Wang, Junli Zhang, Jorge I. Moriconi, German F. Burguener, Leonardo D. Gualano, Tyson Howell, Adam Lukaszewski, Brian Staskawicz, Myeong-Je Cho, Jaclyn Tanaka, Tzion Fahima, Haiyan Ke, Katayoon Dehesh, Guo-Liang Zhang, Jin-Ying Gou, Mats Hamberg, Guillermo E. Santa-María & Jorge Dubcovsky
Wheat, an essential crop for global food security, is well adapted to a wide variety of soils. However, the gene networks shaping different root architectures remain poorly understood. We report here that dosage differences in a cluster of monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) modulate key differences in wheat root architecture, which are associated with grain yield under water-limited conditions. Wheat plants with loss-of-function mutations in OPRIII show longer seminal roots, whereas increased OPRIII dosage or transgenic over-expression result in reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA and JA-Ile). Pharmacological inhibition of JA-biosynthesis abolishes root length differences, consistent with a JA-mediated mechanism. Transcriptome analyses of transgenic and wild-type lines show significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways, which parallel changes in ROS distribution. OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals
12 September 2022 • International Journal of Molecular Sciences
Nikolai Govta, Iris Polda, Hanan Sela, Yafit Cohen, Diane M. Beckles, Abraham B. Korol, Tzion Fahima, Yehoshua Saranga and Tamar Krugman
The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H2 = 0.5–0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 marker-trait associations (MTAs) for yield and quality-related traits, 82 under D and 72 under W, and identified potential candidate genes. We identified 24 accessions showing high and/or stable yields under D conditions that can be recommended for cultivation in regions under the threat of global climate change.
The aim of the present study was to identify the structure of active compounds in Cyathus stratus that previously demonstrated anti-pancreatic cancer activity. The active compounds were purified from a crude extract by a series of RP-18 preparative chromatography using homemade octadecyl silica gel column. HPLC injection of the crude extract revealed a chromatogram with three main peaks with retention times (RT) 15.6, 18.2, and 22.5 min. Each fraction that exhibited promising activity in vitro was further separated using various available chromatographic techniques. The purified compound with the ultimate anti-cancer activity appeared at RT of 15.8 in the HPLC chromatogram with more than 90% purity. The main peak at the mass spectra appeared at m/z = 446.2304 with the calculated molecular formula of C25H34O7. One- and two-dimensional NMR analyses indicated that the structure of the active molecule (peak 15.8 min in HPLC) was identified as striatal C. Exposure of human pancreatic cancer cells to purified striatal C resulted in induction of apoptosis. Further studies are needed in order to develop a method for the synthesis of striatal in order to use it in clinical studies for treatment of cancer.
3 March 2022 • Weed Research
Jackline Abu-Nassar, Shira Gal,Ilana Shtein, Assaf Distelfeld, Maor Matzrafi
Solanum rostratum Dunal is an aggressive invasive weed invading many countries worldwide. Our previous study indicated differences in herbicide response between young and mature plants. In this study, we explore the functional leaf surface anatomy of S. rostratum. Leaf area surface characterisation was performed by counting stomata, stellate and glandular trichomes on upper and lower leaf sides on scanning electron microscopy (SEM) micrographs. Total cuticular waxes were extracted and weighed in young and mature leaves. Young and mature leaves were tested for water permeability of the epidermal surfaces using the apoplastic tracer Calcofluor. S. rostratum plants were sprayed with luminous trace colour solution with and without 1% surfactant, droplet number and area were calculated. In young S. rostratum leaves, the leaf surface was densely covered with stellate trichomes on both leaf sides; however, in the mature leaf, stellate trichomes density became low, and prickle rigid increased in mature leaves. Wax amount was significantly higher in mature leaves, while number of stomata was higher in young leaves. Young leaves showed high leaf permeability, with the fluorescent dye permeating the leaf staining the vascular bundles. In young and mature leaves treated with a spraying solution with the addition of surfactant, low droplet number alongside higher coverage area was recorded. Our data highlight the notable differences in leaf epidermal structure of young versus mature plants. We conclude that differences in herbicide permeability, water loss and herbivory in young versus mature leaves of S. rostratum are governed by variation in leaf functional anatomy.
7 March 2022 • Nature Ecology & Evolution
Gabriela M. Pinho, Julien G. A. Martin, Colin Farrell, Amin Haghani, Joseph A. Zoller, Joshua Zhang, Sagi Snir, Matteo Pellegrini, Robert K. Wayne, Daniel T. Blumstein & Steve Horvath
Species that hibernate generally live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor–arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause ageing suppression. Metabolic rate is also a known correlate of longevity; we thus proposed the ‘hibernation–ageing hypothesis’ whereby ageing is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7–8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females was modelled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic ageing over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (two years old). With respect to circannual patterns, the epigenetic age increased during the active season and essentially stalled during the hibernation period. Taken together, our results are consistent with the hibernation–ageing hypothesis and may explain the enhanced longevity in hibernators.
17 February 2022 • Frontiers in Physiology
Mirko Pegoraro, Emily Sayegh Rezek, Bettina Fishman and Eran Tauber
Cryptochrome (CRY) is a conserved protein associated with the circadian clock in a broad range of organisms, including plants, insects, and mammals. In Drosophila, cry is a pleiotropic gene that encodes a blue light-dedicated circadian photoreceptor, as well as an electromagnetic field sensor and a geotaxis behavior regulator. We have generated a panel of nearly-isogenic strains that originated from various wild populations and which carry different natural alleles of cry. Sequencing of these alleles revealed substantial polymorphism, the functional role of which was elusive. To link this natural molecular diversity to gene function, we relied on association mapping. Such analysis revealed two major haplogroups consisting of six linked nucleotides associated with circadian phase (haplotypes All1/All2). We also generated a maximum-likelihood gene-tree that uncovered an additional pair of haplogroups (B1/B2). Behavioral analysis of the different haplotypes indicated significant effect on circadian phase and period, as well on the amount of activity and sleep. The data also suggested substantial epistasis between the All and B haplogroups. Intriguingly, circadian photosensitivity, assessed by light-pulse experiments, did not differ between the genotypes. Using CRISPR-mediated transgenic flies, we verified the effect of B1/B2 polymorphism on circadian phase. The transgenic flies also exhibited substantially different levels of cry transcription. We, moreover, analyzed the geographical distribution of the B1/B2 haplotypes, focusing on a 12 bp insertion/deletion polymorphism that differentiates the two haplotypes. Analysis of cry sequences in wild populations across Europe revealed a geographical cline of B1/B2 indel frequency, which correlated with seasonal bioclimatic variables. This spatial distribution of cry polymorphism reinforces the functional importance of these haplotypes in the circadian system and local adaptation.
Stripe rust is a devastating disease in wheat that causes substantial yield loss around the world. The most effective strategy for mitigating yield loss is to develop resistant cultivars. The wild relatives of wheat are good sources of resistance to fungal pathogens. Here, we used a genome-wide association study (GWAS) to identify loci associated with stripe rust (causal agent: Puccinia striiformis f. sp. tritici) resistance in wild emmer (Triticum dicoccoides) at the seedling stage, in the greenhouse, and at the adult plant stage, in the field. We found that the two major loci contributing to resistance in our wild emmer panel were the previously cloned seedling-stage resistance gene, Yr15, and the adult-plant-stage resistance gene, Yr36. Nevertheless, we detected 12 additional minor QTLs that additionally contribute to adult plant resistance and mapped a locus on chromosome 3AS that tentatively harbors a novel seedling resistance gene. The genotype and phenotype data generated for the wild emmer panel, together with the detected SNPs associated with resistance to stripe rust, provide a valuable resource for disease-resistance breeding in durum and bread wheat
27 February 2022 • Applied Microbiology
Based on the collected data on the diversity of microalgae and environmental indicators in dry and wet seasons during 2011–2018, from 45 samples, 59 species of microalgae were identified in the ornithological object—Lake Agmon in the Hula Valley. In the samples of periphyton and microphytobenthos, diatoms predominated. Bioindication analysis and statistical mapping revealed the most pronounced zones of influence on the lake ecosystem, as well as indicators of the environment and diversity that clearly demonstrate them. The correlation between the distribution of TDS of water over the lake surface and the distribution of green, diatom microalgae and cyanobacteria detected two areas of impact from the old channel of the Jordan River in the northwestern part and from the drainage channel in the northeastern parts of the lake. The area on the east coast, in contact with the resting fields of migratory birds, has provided nutrients that stimulate the development of green algae and cyanobacteria. This showed implicit links in the lake ecosystem using bioindicators make it possible to recommend them for monitoring in combination with statistical mapping, which visualizes the distribution of data and is easily accessible for the decision-making system for the management of a protected ornithological lake
While it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the 'HbS mutation' when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible
Cylindrospermopsis raciborskii is a central bloom-forming cyanobacteria. However, despite its ecological significance, little is known of its interactions with the phages that infect it. Currently only a single sequenced genome of a Cylindrospermopsis-infecting phage is publicly available. Here we describe the isolation and characterization of Cr-LKS3, a second phage infecting Cylindrospermopsis. Cr-LKS3 is a siphovirus with a higher genome similarity to prophages within heterotrophic bacteria genomes than to any other cyanophage/cyano-prophage, suggesting that it represents a novel cyanophage group. The function, order and orientation of the 72 genes in the Cr-LKS3 genome are highly similar to those of Escherichia virus Lambda (hereafter Lambda), despite the very low sequence similarity between these phages, showing high evolutionary convergence despite the substantial difference in host characteristics. Similarly to Lambda, the genome of Cr-LKS3 contains various genes that are known to be central to lysogeny, suggesting it can enter a lysogenic cycle. Cr-LKS3 has a unique ability to infect a host with a dramatically different GC content, without carrying any tRNA genes to compensate for this difference. This ability, together with its potential lysogenic lifestyle shed light on the complex interactions between C. raciborskii and its phages
21 January 2022 • Journal of Fungi
Alona Yu. Biketova, Matteo Gelardi, Matthew E. Smith, ...,Solomon P. Wasser, Ursula Peintner, Eviatar Nevo, Britt A. Bunyard and Alfredo Vizzini
The boletoid genera Butyriboletus and Exsudoporus have recently been suggested by some researchers to constitute a single genus, and Exsudoporus was merged into Butyriboletus as a later synonym. However, no convincing arguments have yet provided significant evidence for this congeneric placement. In this study, we analyze material from Exsudoporus species and closely related taxa to assess taxonomic and phylogenetic boundaries between these genera and to clarify species delimitation within Exsudoporus. Outcomes from a multilocus phylogenetic analysis (ITS, nrLSU, tef1-α and rpb2) clearly resolve Exsudoporus as a monophyletic, homogenous and independent genus that is sister to Butyriboletus. An accurate morphological description, comprehensive sampling, type studies, line drawings and a historical overview on the nomenclatural issues of the type species E. permagnificus are provided. Furthermore, this species is documented for the first time from Israel in association with Quercus calliprinos. The previously described North American species Exsudoporus frostii and E. floridanus are molecularly confirmed as representatives of Exsudoporus, and E. floridanus is epitypified. The eastern Asian species Leccinum rubrum is assigned here to Exsudoporus based on molecular evidence, and a new combination is proposed. Sequence data from the original material of the Japanese Boletus kermesinus were generated, and its conspecificity with L. rubrum is inferred as formerly presumed based on morphology. Four additional cryptic species from North and Central America previously misdetermined as either B. frostii or B. floridanus are phylogenetically placed but remain undescribed due to the paucity of available material. Boletus weberi (syn. B. pseudofrostii) and Xerocomus cf. mcrobbii cluster outside of Exsudoporus and are herein assigned to the recently described genus Amoenoboletus. Biogeographic distribution patterns are elucidated, and a dichotomous key to all known species of Exsudoporus worldwide is presented.