scholarly journals Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum

2020 ◽  
Vol 11 ◽  
Author(s):  
Dong Liang ◽  
Christian Benjamin Andersen ◽  
Ramesh R. Vetukuri ◽  
Daolong Dou ◽  
Laura J. Grenville-Briggs
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plant Pathogens ◽  
Tandem Duplication ◽  
Crop Protection ◽  
Rapid Evolution ◽  
Gene Families ◽  
Plant Diseases ◽  
Pythium Oligandrum ◽  
Fungal Cell

Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum, have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species (P. oligandrum and P. periplocum), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection

2020 ◽  
Vol 17 (4) ◽  
pp. 1434
Author(s):  
Deepti Malviya ◽  
Pramod Kumar Sahu ◽  
Udai B. Singh ◽  
Surinder Paul ◽  
Amrita Gupta ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
Plant Pathogens ◽  
Antimicrobial Agents ◽  
Plant Protection ◽  
Crop Protection ◽  
Emerging Diseases ◽  
Plant Diseases ◽  
Effective Control ◽  
Biological Pest Control ◽  
Biofilm Inhibition

Microorganisms area treasure in terms of theproduction of various bioactive compounds which are being explored in different arenas of applied sciences. In agriculture, microbes and their bioactive compounds are being utilized in growth promotion and health promotion withnutrient fortification and its acquisition. Exhaustive explorations are unraveling the vast diversity of microbialcompounds with their potential usage in solving multiferous problems incrop production. Lipopeptides are one of such microbial compounds which havestrong antimicrobial properties against different plant pathogens. These compounds are reported to be produced by bacteria, cyanobacteria, fungi, and few other microorganisms; however, genus Bacillus alone produces a majority of diverse lipopeptides. Lipopeptides are low molecular weight compounds which havemultiple industrial roles apart from being usedas biosurfactants and antimicrobials. In plant protection, lipopeptides have wide prospects owing totheirpore-forming ability in pathogens, siderophore activity, biofilm inhibition, and dislodging activity, preventing colonization bypathogens, antiviral activity, etc. Microbes with lipopeptides that haveall these actions are good biocontrol agents. Exploring these antimicrobial compounds could widen the vistasof biological pest control for existing and emerging plant pathogens. The broader diversity and strong antimicrobial behavior of lipopeptides could be a boon for dealing withcomplex pathosystems and controlling diseases of greater economic importance. Understanding which and how these compounds modulate the synthesis and production of defense-related biomolecules in the plants is a key question—the answer of whichneeds in-depth investigation. The present reviewprovides a comprehensive picture of important lipopeptides produced by plant microbiome, their isolation, characterization, mechanisms of disease control, behavior against phytopathogens to understand different aspects of antagonism, and potential prospects for future explorations as antimicrobial agents. Understanding and exploring the antimicrobial lipopeptides from bacteria and fungi could also open upan entire new arena of biopesticides for effective control of devastating plant diseases.

scholarly journals Inducing Fungus-Resistance into Plants through Biotechnology

2010 ◽  
Vol 2 (2) ◽  
pp. 14-21 ◽  
Author(s):  
Shabir Hussain WANI
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Hydrolytic Enzymes ◽  
Defense Responses ◽  
Stilbene Synthase ◽  
Fungal Disease ◽  
Plant Diseases ◽  
Fungal Cell ◽  
Oxidase Gene ◽  
Enhanced Resistance

Plant diseases are caused by a variety of plant pathogens including fungi, and their management requires the use of techniques like transgenic technology, molecular biology, and genetics. There have been attempts to use gene technology as an alternative method to protect plants from microbial diseases, in addition to the development of novel agrochemicals and the conventional breeding of resistant cultivars. Various genes have been introduced into plants, and the enhanced resistance against fungi has been demonstrated. These include: genes that express proteins, peptides, or antimicrobial compounds that are directly toxic to pathogens or that reduce their growth in situ; gene products that directly inhibit pathogen virulence products or enhance plant structural defense genes, that directly or indirectly activate general plant defense responses; and resistance genes involved in the hypersensitive response and in the interactions with virulence factors. The introduction of the tabtoxin acetyltransferase gene, the stilbene synthase gene, the ribosome-inactivation protein gene and the glucose oxidase gene brought enhanced resistance in different plants. Genes encoding hydrolytic enzymes such as chitinase and glucanase, which can deteriorate fungal cell-wall components, are attractive candidates for this approach and are preferentially used for the production of fungal disease-resistant plants. In addition to this, RNA-mediated gene silencing is being tried as a reverse tool for gene targeting in plant diseases caused by fungal pathogens. In this review, different mechanisms of fungal disease resistance through biotechnological approaches are discussed and the recent advances in fungal disease management through transgenic approach are reviewed.

scholarly journals Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

2020 ◽  
Vol 12 (4) ◽  
pp. 381-395
Author(s):  
Nilson Da Rocha Coimbra ◽  
Aristoteles Goes-Neto ◽  
Vasco Azevedo ◽  
Aïda Ouangraoua
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Gene Tree ◽  
Gene Families ◽  
Common Mechanism ◽  
Species Trees ◽  
Bacterial Phylogeny ◽  
Homologous Genes

Abstract Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

scholarly journals Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell

1999 ◽  
Vol 9 (7) ◽  
pp. 608-628 ◽  
Author(s):  
Kira S. Makarova ◽  
L. Aravind ◽  
Michael Y. Galperin ◽  
Nick V. Grishin ◽  
Roman L. Tatusov ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Families ◽  
Small Subset ◽  
Specific Gene ◽  
Genome Replication ◽  
Protein Families ◽  
Archaeal Protein ◽  
The Core ◽  
Stable Core

Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, andPyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. The proteins that belong to these conserved euryarchaeal families comprise 31%–35% of the gene complement and may be considered the evolutionarily stable core of the archaeal genomes. The core gene set includes the great majority of genes coding for proteins involved in genome replication and expression, but only a relatively small subset of metabolic functions. For many gene families that are conserved in all euryarchaea, previously undetected orthologs in bacteria and eukaryotes were identified. A number of euryarchaeal synapomorphies (unique shared characters) were identified; these are protein families that possess sequence signatures or domain architectures that are conserved in all euryarchaea but are not found in bacteria or eukaryotes. In addition, euryarchaea-specific expansions of several protein and domain families were detected. In terms of their apparent phylogenetic affinities, the archaeal protein families split into bacterial and eukaryotic families. The majority of the proteins that have only eukaryotic orthologs or show the greatest similarity to their eukaryotic counterparts belong to the core set. The families of euryarchaeal genes that are conserved in only two or three species constitute a relatively mobile component of the genomes whose evolution should have involved multiple events of lineage-specific gene loss and horizontal gene transfer. Frequently these proteins have detectable orthologs only in bacteria or show the greatest similarity to the bacterial homologs, which might suggest a significant role of horizontal gene transfer from bacteria in the evolution of the euryarchaeota.

scholarly journals Allelopathy and Agricultural Sustainability: Implication in weed management and crop protection—an overview

2019 ◽  
Vol 5 (2) ◽  
pp. 54-61
Author(s):  
Zahir Muhammad ◽  
Naila Inayat ◽  
Abdul Majeed ◽  
Hazrat Ali ◽  
Kaleem Ullah ◽  
...  
Keyword(s):  
Weed Management ◽  
Crop Production ◽  
Plant Pathogens ◽  
Crop Protection ◽  
Soil Health ◽  
Crop Plants ◽  
Plant Diseases ◽  
Agricultural Sustainability ◽  
Biotic And Abiotic Stresses ◽  
Diverse Plant

Abstract Crop plants have defined roles in agricultural production and feeding the world. They are affected by several environmental and biological stresses, which range from soil salinity, drought, and climate change to exposure to diverse plant pathogens. These stresses pose risk to agricultural sustainability. To avoid the increasing biotic and abiotic pressure on crop plants, agrochemicals are extensively used in agriculture for attaining desirable yield and production of crops. However, the use of agrochemicals is also challenging the integrity of ecosystems. Thus, to maintain the integrity of ecosystem, sustainable measures for elevated crop production are required. Allelopathy, a process of chemical interactions between plants and other organisms, could be used in the management of several biotic and abiotic stresses if the basic mechanisms of the phenomena and plants with allelopathic potentials are known. Allelopathy has a promising future for its application in agriculture for natural weed management, improving soil health and suppressing plant diseases. The aim of this review is to discuss the importance of allelopathy in agriculture and its role in sustainability with a specific focus on weed management and crop protection.

scholarly journals Adaptive evolution of hybrid bacteria by horizontal gene transfer

2021 ◽  
Vol 118 (10) ◽  
pp. e2007873118
Author(s):  
Jeffrey J. Power ◽  
Fernanda Pinheiro ◽  
Simone Pompei ◽  
Viera Kovacova ◽  
Melih Yüksel ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Adaptive Evolution ◽  
Gene Networks ◽  
Fitness Landscape ◽  
Parallel Evolution ◽  
Rapid Evolution ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Stationary Growth Phase

Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.

scholarly journals Rapid evolution and horizontal gene transfer in the genome of a male-killing Wolbachia

2020 ◽  
Author(s):  
Tom Hill ◽  
Robert L. Unckless ◽  
Jessamyn I. Perlmutter
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Species ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Rapid Evolution ◽  
Male Killing ◽  
Show Evidence ◽  
Bacterial Endosymbionts ◽  
Unique Genes

AbstractWolbachia are widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains of Wolbachia have some striking effects on their hosts. In some cases, these symbionts manipulate host reproduction to increase the fitness of infected, transmitting females. Here we examine the genome and population genomics of a male-killing Wolbachia strain, wInn, that infects Drosophila innubila mushroom-feeding flies. We compared wInn to other closely-related Wolbachia genomes to understand the evolutionary dynamics of specific genes. The wInn genome is similar in overall gene content to wMel, but also contains many unique genes and repetitive elements that indicate distinct gene transfers between wInn and non-Drosophila hosts. We also find that genes in the Wolbachia prophage and Octomom regions are particularly rapidly evolving, including those putatively or empirically confirmed to be involved in host pathogenicity. Of the genes that rapidly evolve, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes, suggesting frequent movement of rapidly evolving regions among individuals. These dynamics of rapid evolution and horizontal gene transfer across the genomes of several Wolbachia strains and divergent host species may be important underlying factors in Wolbachia’s global success as a symbiont.

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