Key Insights and Research Prospects at the Dawn of the Population Genomics Era for Verticillium dahliae

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Jie-Yin Chen ◽  
Steven J. Klosterman ◽  
Xiao-Ping Hu ◽  
Xiao-Feng Dai ◽  
Krishna V. Subbarao
Keyword(s):  
Population Structure ◽  
Verticillium Dahliae ◽  
Plant Pathogens ◽  
Population Genomics ◽  
Population Divergence ◽  
Annual Review ◽  
Publication Date ◽  
Disease Symptoms ◽  
Historical Perspectives ◽  
Characteristic Features

The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species. Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Alexandra J. Weisberg ◽  
Niklaus J. Grünwald ◽  
Elizabeth A. Savory ◽  
Melodie L. Putnam ◽  
Jeff H. Chang
Keyword(s):  
Disease Surveillance ◽  
Plant Pathogens ◽  
Response Times ◽  
Great Promise ◽  
Annual Review ◽  
Publication Date ◽  
Data Sets ◽  
Complex Data ◽  
Significant Cost ◽  
Complex Data Sets

Diseases have a significant cost to agriculture. Findings from analyses of whole-genome sequences show great promise for informing strategies to mitigate risks from diseases caused by phytopathogens. Genomic approaches can be used to dramatically shorten response times to outbreaks and inform disease management in novel ways. However, the use of these approaches requires expertise in working with big, complex data sets and an understanding of their pitfalls and limitations to infer well-supported conclusions. We suggest using an evolutionary framework to guide the use of genomic approaches in epidemiology and diagnostics of plant pathogens. We also describe steps that are necessary for realizing these as standard approaches in disease surveillance. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

What Have We Learned from the First 500 Avian Genomes?

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Gustavo A. Bravo ◽  
C. Jonathan Schmitt ◽  
Scott V. Edwards
Keyword(s):  
Population Genomics ◽  
Sequence Data ◽  
Genome Project ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Bird Diversity ◽  
Annual Review ◽  
Publication Date ◽  
Genomic Changes ◽  
Rare Genomic Changes

The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Emerging Roles of Posttranslational Modifications in Plant-Pathogenic Fungi and Bacteria

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Wende Liu ◽  
Lindsay Triplett ◽  
Xiao-Lin Chen
Keyword(s):  
Posttranslational Modifications ◽  
Protein Function ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Annual Review ◽  
Publication Date ◽  
Plant Pathogenic Fungi ◽  
Plant Interactions ◽  
Host Infection ◽  
Infection Processes

Posttranslational modifications (PTMs) play crucial roles in regulating protein function and thereby control many cellular processes and biological phenotypes in both eukaryotes and prokaryotes. Several recent studies illustrate how plant fungal and bacterial pathogens use these PTMs to facilitate development, stress response, and host infection. In this review, we discuss PTMs that have key roles in the biological and infection processes of plant-pathogenic fungi and bacteria. The emerging roles of PTMs during pathogen–plant interactions are highlighted. We also summarize traditional tools and emerging proteomics approaches for PTM research. These discoveries open new avenues for investigating the fundamental infection mechanisms of plant pathogens and the discovery of novel strategies for plant disease control. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Models of Plant Resistance Deployment

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Loup Rimbaud ◽  
Frédéric Fabre ◽  
Julien Papaïx ◽  
Benoît Moury ◽  
Christian Lannou ◽  
...  
Keyword(s):  
Plant Resistance ◽  
Plant Pathogens ◽  
Gene Pyramiding ◽  
Resistance Management ◽  
Specific Model ◽  
Annual Review ◽  
Publication Date ◽  
Evolutionary Potential ◽  
Control Cost ◽  
Spatiotemporal Scales

Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
William J. Murphy ◽  
Nicole M. Foley ◽  
Kevin R. Bredemeyer ◽  
John Gatesy ◽  
Mark S. Springer
Keyword(s):  
Genetic Architecture ◽  
Placental Mammal ◽  
Population Divergence ◽  
Annual Review ◽  
Publication Date ◽  
Closely Related Species ◽  
Genome Data ◽  
The Rich ◽  
Interspecific Comparisons ◽  
Genome Assemblies

The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole-genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Neha Potnis
Keyword(s):  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Management Strategies ◽  
Annual Review ◽  
Past Century ◽  
Publication Date ◽  
Significant Shift ◽  
Xanthomonas Perforans ◽  
Disease Resistant ◽  
Microbe Interactions

Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant–microbe interactions for this pathosystem to tailor disease management strategies. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jie-Yin Chen ◽  
Dan-Dan Zhang ◽  
Jin-Qun Huang ◽  
Ran Li ◽  
Dan Wang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Verticillium Dahliae ◽  
Plant Pathogens ◽  
Population Genomics ◽  
De Novo ◽  
Sequence Divergence ◽  
Parental Genome ◽  
Nucleotide Polymorphisms ◽  
Agricultural Ecosystems ◽  
Race 1

Abstract Background Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment. Results In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation. Conclusions Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

scholarly journals Skipping the Insect Vector: Plant Stolon Transmission of the Phytopathogen ‘Ca. Phlomobacter fragariae’ from the Arsenophonus Clade of Insect Endosymbionts

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 93
Author(s):  
Jessica Dittmer ◽  
Thierry Lusseau ◽  
Xavier Foissac ◽  
Franco Faoro
Keyword(s):  
Plant Pathogens ◽  
Model Systems ◽  
Insect Vector ◽  
Evolutionary Perspective ◽  
Evolutionary Transition ◽  
Strawberry Plant ◽  
Disease Symptoms ◽  
Transmission Electron ◽  
Nutrient Provisioning ◽  
Early Growth Phase

The genus Arsenophonus represents one of the most widespread clades of insect endosymbionts, including reproductive manipulators and bacteriocyte-associated primary endosymbionts. Two strains belonging to the Arsenophonus clade have been identified as insect-vectored plant pathogens of strawberry and sugar beet. The bacteria accumulate in the phloem of infected plants, ultimately causing leaf yellows and necrosis. These symbionts therefore represent excellent model systems to investigate the evolutionary transition from a purely insect-associated endosymbiont towards an insect-vectored phytopathogen. Using quantitative PCR and transmission electron microscopy, we demonstrate that ‘Candidatus Phlomobacter fragariae’, bacterial symbiont of the planthopper Cixius wagneri and the causative agent of Strawberry Marginal Chlorosis disease, can be transmitted from an infected strawberry plant to multiple daughter plants through stolons. Stolons are horizontally growing stems enabling the nutrient provisioning of daughter plants during their early growth phase. Our results show that Phlomobacter was abundant in the phloem sieve elements of stolons and was efficiently transmitted to daughter plants, which rapidly developed disease symptoms. From an evolutionary perspective, Phlomobacter is, therefore, not only able to survive within the plant after transmission by the insect vector, but can even be transmitted to new plant generations, independently from its ancestral insect host.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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