Article
Plant Sciences
Yuan Jiang, Zhixue Wang, Hui Du, Runlong Dong, Yaping Yuan, Jian Hua
Summary: This study analyzed the functional relevance of gene variants associated with local temperature variation in Arabidopsis thaliana, and found that genes associated with maximum temperature are more likely to function at higher temperatures, while genes associated with minimum temperature are more likely to function at lower temperatures. The research also showed that gene variants are distributed more frequently at geographic locations where they offer enhanced growth or tolerance.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Gerardo Arceo-Gomez
Summary: The study reveals that heterospecific pollen transfer can directly influence plant interactions and play a significant role in generating plant diversity. The existence of spatial variation has important implications for the interactions between species within plant communities and deserves further investigation.
Article
Biochemistry & Molecular Biology
Paul F. Gugger, Sorel T. Fitz-Gibbon, Ana Albarran-Lara, Jessica W. Wright, Victoria L. Sork
Summary: Understanding how the environment shapes genetic variation is crucial for studying the evolution of local adaptation. Through landscape genomic approaches, researchers identified genetic variation underlying local adaptation in California endemic oak, Quercus lobata, and found evidence of natural selection at multiple spatial scales. The study provides robust evidence for novel candidate genes for local climate adaptation across different spatial scales.
Review
Plant Sciences
Maarten Koornneef
Summary: The author's involvement in the development of genetics within the integrated study of plant biology is founded on education as a plant breeder and collaborations with plant physiologists and molecular geneticists. Research initially focused on mutants related to plant hormones, photoreceptors, and flowering time in Arabidopsis and tomato, alongside the genetic mapping of Arabidopsis. Subsequent interest in natural variation and molecular identification of genetic differences, as well as the adoption of Arabidopsis as a model species, significantly contributed to progress in plant biology knowledge over the past 40 years.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021
(2021)
Article
Biochemistry & Molecular Biology
Yu Okamura, Ai Sato, Lina Kawaguchi, Atsushi J. Nagano, Masashi Murakami, Heiko Vogel, Juergen Kroymann
Summary: Herbivorous insects have evolved counteradaptations to overcome chemical defences of their host plants. The diversity of host plants shapes the diversity of insect counteradaptations. Different butterfly species show different patterns of host plant use and adaptation.
Article
Biochemistry & Molecular Biology
Bret A. Payseur, Peicheng Jing
Summary: By studying the genomes of house mice that invaded Gough Island, researchers identified numerous windows showing strong evidence for positive selection, with genes related to exploratory behavior and body size being potential targets. These selection windows contain genes with derived nonsynonymous mutations and over-represented gene ontologies emphasizing neurological themes. This study provides insights into the genetic basis of adaptation to island conditions and establishes Gough Island mice as a valuable system for studying natural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Li-Na Yang, Haibing Ouyang, Oswald Nkurikiyimfura, Hanmei Fang, Abdul Waheed, Wenyang Li, Yan-Ping Wang, Jiasui Zhan
Summary: Investigating the impact of environmental factors on plant diseases, a study revealed the significant role of climate conditions in the evolution of effector genes. By sampling and sequencing populations of Phytophthora infestans, it was found that the effector gene Pi02860 exhibited moderate genetic variation influenced by altitude and experimental temperature.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Isai Salas-Gonzalez, Guilhem Reyt, Paulina Flis, Valeria Custodio, David Gopaulchan, Niokhor Bakhoum, Tristan P. Dew, Kiran Suresh, Rochus Benni Franke, Jeffery L. Dangl, David E. Salt, Gabriel Castrillo
Summary: Plant roots and animal guts have evolved specialized cell layers to control mineral nutrient homeostasis, tolerating resident microbiota while keeping integrity. In the model plant Arabidopsis thaliana, genes controlling endodermal function contribute to plant microbiome assembly, driven by a regulatory mechanism of endodermal differentiation with profound effects on nutrient homeostasis. This mechanism is linked to the microbiota's capacity to repress responses to the phytohormone abscisic acid in the root, establishing the endodermis as a regulatory hub coordinating microbiota assembly and homeostatic mechanisms.
Article
Multidisciplinary Sciences
Dolph Schluter, Kerry B. Marchinko, Matthew E. Arnegard, Haili Zhang, Shannon D. Brady, Felicity C. Jones, Michael A. Bell, David M. Kingsley
Summary: Most mutations for adaptation to new environments are small-effect, but large-effect beneficial variants can contribute significantly under certain conditions. A study on stickleback populations showed that an ancient freshwater allele near the Eda gene had a large fitness effect, leading to a significant increase in offspring survival and allele frequency in freshwater environments. The findings suggest strong selection on this gene (and/or linked genes) in freshwater habitats, which may increase the prevalence of large-effect fitness variants in adaptive evolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Joris Macquet, Shantala Mounichetty, Sylvain Raffaele
Summary: Plants and pathogens engage in a coevolutionary arms race, leading to diversification and specialization of genes involved in resistance and virulence. Major innovations in plant-pathogen interactions have emerged through the expansion of gene function. Understanding these molecular mechanisms is crucial for the functional and predictive biology of plant-pathogen interactions.
TRENDS IN PLANT SCIENCE
(2022)
Article
Microbiology
E-Jiao Wu, Yan-Ping Wang, Li-Na Yang, Mi-Zhen Zhao, Jiasui Zhan
Summary: Understanding pathogen adaptation to global warming is crucial for predicting disease epidemics and agricultural production in the future. This study used a combination of population genetics, physiological assays, and common garden experiments to analyze the genetic and physiological characteristics of 140 Phytophthora infestans genotypes under different temperature regimes. The results showed that pathogens from warmer regions had a higher thermal preference and broader thermal niche compared to those from cooler regions. Phenotypic plasticity played a more important role than genetic variance in determining aggressiveness. Experimental temperatures also influenced the expression of genetic variation and the association between pathogen aggressiveness and local temperature. These findings highlight the importance of including geographic variation in pathogen thermal preferences in modeling future disease epidemics in response to global warming.
Review
Plant Sciences
Eleni Koseoglou, Jan M. van der Wolf, Richard G. F. Visser, Yuling Bai
Summary: Plants have developed complex defense mechanisms to resist pathogens, but pathogens can use effector proteins to manipulate plant susceptibility genes, rendering defenses ineffective. Identification and mutation of plant susceptibility genes utilized by bacterial pathogens are crucial for breeding durable and broad-spectrum resistant crops. New genome editing technologies offer new possibilities for modifying susceptibility genes.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kathrin A. Otte
Summary: This article presents a new approach to genotype-environment association (GEA) studies called genomic window analysis, which combines the information of neighboring single-nucleotide polymorphisms (SNPs) to enhance the detection of genomic signals of environmental adaptation. The method is proven to be superior to several established GEA approaches, especially in cases with small sample sizes, through simulations and real data analysis.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Plant Sciences
Yi Liu, Danyu Kong, Hui-Lan Wu, Hong-Qing Ling
Summary: This article discusses the important role of iron in plant-pathogen interactions and how plants and pathogens regulate iron levels to maintain fitness. It also proposes directions for future research on this topic.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Plant Sciences
Siyu Song, Yang Liu, Nicole R. Wang, Cara H. Haney
Summary: The use of genetically tractable plant-microbe pairs has significantly advanced research in plant immunity and mutualistic symbiosis. However, the complexity of the microbiome and its subtle effects on plant growth and immunity have hindered forward genetic screening to identify genes shaping the microbiome. Research in microbiome has largely relied on reverse genetics approaches based on plant nutrient uptake and immunity knowledge.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Joanna L. Rifkin, Felix E. G. Beaudry, Zoe Humphries, Baharul Choudhury, Spencer C. H. Barrett, Stephen Wright
Summary: The study suggests that low recombination rates may precede the formation of sex-linked regions, with large regions of recombination suppression found across all chromosomes. Additionally, gene and repetitive sequence density are correlated with recombination rates, with the variation patterns differing by repetitive element type.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Ecology
Stephen I. Wright
Article
Biochemistry & Molecular Biology
Julia M. Kreiner, Patrick J. Tranel, Detlef Weigel, John R. Stinchcombe, Stephen I. Wright
Summary: This study used genome-wide association and population genomic approaches to identify 250 genes associated with non-target-site resistance. These genes, found across different chromosomes, suggest a diverse and population-specific genetic architecture of herbicide resistance.
Article
Biochemistry & Molecular Biology
George Sandler, Stephen Wright, Aneil F. Agrawal
Summary: Most types of mutations exhibit positive linkage disequilibrium, especially if they are predicted to be less deleterious. Through simulations, it has been shown that this pattern arises easily in a model of admixture or distance-biased mating. Additionally, loss of function mutations exhibit particularly positive LD across short distances.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Robert Horvath, Emily B. Josephs, Edouard Pesquet, John R. Stinchcombe, Stephen Wright, Douglas Scofield, Tanja Slotte
Summary: This study focused on identifying functional noncoding regions in Capsella grandiflora and estimating selection pressures on these regions. Results showed that these regions harbor a significant amount of weakly and strongly deleterious mutations, shedding light on the role of selection in evolutionary processes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Kimberly Skead, Armande Ang Houle, Sagi Abelson, Mawusse Agbessi, Vanessa Bruat, Boxi Lin, David Soave, Liran Shlush, Stephen Wright, John Dick, Quaid Morris, Philip Awadalla
Summary: The authors investigate how the interplay of positive and negative selection influences AML progression using deep learning and population genetics models. They find that purifying selection plays a critical role in preventing disease-predisposing clones from rising to dominance.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Julia M. Kreiner, Amalia Caballero, Stephen Wright, John R. Stinchcombe
Summary: The invasion of Amaranthus tuberculatus into agricultural environments has led to significant adaptive differences, with a preference for southwestern var. rudis ancestry resulting in higher biomass and treatment-specific phenotypes. Additionally, individuals in agricultural habitats exhibit de novo adaptation independent of ancestry effects.
Article
Biology
Julia M. Kreiner, George Sandler, Aaron J. Stern, Patrick J. Tranel, Detlef Weigel, John R. Stinchcombe, Stephen Wright
Summary: This study investigates the evolutionary history of herbicide resistance in agricultural fields using genomic data from common waterhemp populations. The researchers find that resistance alleles show strong parallelism in their mutational origins and are influenced by gene flow in their distribution. The age and selection dynamics of resistant lineages vary, indicating heterogeneity in the forces that govern their persistence, including intra- and inter-locus allelic interactions.
Article
Biochemistry & Molecular Biology
Felix E. G. Beaudry, Joanna L. Rifkin, Amanda L. Peake, Deanna Kim, Madeline Jarvis-Cross, Spencer C. H. Barrett, Stephen Wright
Summary: This study investigates the gene flow between different geographic types of the plant species Rumex hastatulus, revealing that hybrids readily form and survive multiple backcross generations in the field. The study also suggests that the neo-sex chromosomes play a role in reproductive isolation between different geographic types.
Article
Biology
Joanna L. Rifkin, Solomiya Hnatovska, Meng Yuan, Bianca M. Sacchi, Baharul Choudhury, Yunchen Gong, Pasi Rastas, Spencer C. H. Barrett, Stephen Wright
Summary: There is growing evidence for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences are still poorly understood. This study provides evidence and characterization of sex differences in recombination landscape in a dioecious plant, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Amandine Cornille, Mathieu Tiret, Adriana Salcedo, Huirun R. Huang, Marion Orsucci, Pascal Milesi, Dmytro Kryvokhyzha, Karl Holm, Xue-Jun Ge, John R. Stinchcombe, Sylvain Glemin, Stephen Wright, Martin Lascoux
Summary: The respective role of demography, plasticity and adaptation in the colonization success of plant species was investigated. It was found that both demography and high phenotypic plasticity contribute to the success of the tetraploid and self-fertilizing species, Capsella bursa-pastoris. The study provides insights into the ecological success of a plant species during range expansion.
Article
Biochemistry & Molecular Biology
Nicolay Leme da Cunha, Haoran Xue, Stephen Wright, Spencer C. H. Barrett
Summary: This study compares the genetic diversity of two related water hyacinth species, E. crassipes and E. azurea, and finds that the highly clonal E. crassipes exhibits lower clonal diversity and weaker genetic structure compared to the moderately clonal E. azurea.
Article
Multidisciplinary Sciences
Julia M. Kreiner, Sergio M. Latorre, Hernan A. Burbano, John R. Stinchcombe, Sarah P. Otto, Detlef Weigel, Stephen I. Wright
Summary: This study uses genome analysis of the common waterhemp to demonstrate the significant impact of modern agriculture and agricultural intensification on the evolution of agricultural weeds. The strong selection pressure and changes in allele frequency trajectories since the 1960s have influenced the success of this weed in the 21st century, with human-mediated range shifts playing a role.
Article
Evolutionary Biology
George Sandler, Aneil F. Agrawal, Stephen Wright
Summary: This study examines the genetic diversity of the facultatively sexual liverwort Marchantia polymorpha and finds no evidence of strictly clonal descent or isolation by distance. Instead, evidence of recent recombination and gene flow between geographically distant isolates suggests a modest frequency of sexual reproduction. However, the genome of M. polymorpha has low levels of nucleotide diversity and signs of inefficient selection, indicating possible linked selection and a small effective population size due to asexual propagation. Overall, the genome reveals a complex history of both sexual and asexual reproduction in M. polymorpha.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Jean Carlier, Francois Bonnot, Veronique Roussel, Sebastien Ravel, Reina Teresa Martinez, Luis Perez-Vicente, Catherine Abadie, Stephen Wright
Summary: This study revealed the genomic basis of adaptation to quantitative resistance in the banana pathogen Pseudocercospora fijiensis, detecting several genomic regions potentially involved in quantitative pathogenicity and highlighting specific host-pathogen interactions. The findings suggest a polygenic basis for fungal adaptation to quantitative plant resistance and complex molecular interactions between plants and pathogens in quantitative disease development.