scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2020 ◽  
Vol 33 (8) ◽  
pp. 1046-1058 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Wenwu Ye ◽  
Yuee Tian ◽  
Yaxin Du ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
De Novo ◽  
Biological Control Agent ◽  
Protein Structures ◽  
Control Agent ◽  
Phytophthora Species ◽  
Host Cells ◽  
Pythium Species ◽  
Origin And Evolution ◽  
Rxlr Effectors

RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2019 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Yuee Tian ◽  
Wenwu Ye ◽  
Hai Zhu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Plant Pathogens ◽  
Genome Rearrangement ◽  
Common Ancestor ◽  
De Novo ◽  
Protein Structures ◽  
Plant Diseases ◽  
Biocontrol Agents ◽  
Ecological Niches ◽  
Rxlr Effectors

AbstractBeing widely existed in oomycetes, the RXLR effector features conserved RXLR-dEER motifs in its N terminal. Every known Phytophthora or Hyaloperonospora pathogen harbors hundreds of RXLRs. In Pythium species, however, none of the RXLR effectors has been characterized yet. Here, we developed a stringent method for de novo identification of RXLRs and characterized 359 putative RXLR effectors from nine tested Pythium species. Phylogenetic analysis revealed a single superfamily formed by all oomycetous RXLRs, suggesting they descent from a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures and genome locations. In particular, the mosquito biological agent P. guiyangense contains a significantly larger RXLR repertoire than the other eight Pythium species examined, which may result from gene duplication and genome rearrangement events as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts from the vast majority of predicted RXLRs with some of them being induced at infection stages. One such RXLRs showed necrosis-inducing activity. Furthermore, all predicted RXLRs were cloned from two biocontrol agents P. oligandrum and P. periplocum. Three of them were found to encode effectors inducing defense response in Nicotiana benthamiana. Taken together, our findings represent the first complete synopsis of Pythium RXLR effectors, which provides critical clues on their evolutionary patterns as well as the mechanisms of their interactions with diverse hosts.Author summaryPathogens from the Pythium genus are widespread across multiple ecological niches. Most of them are soilborne plant pathogens whereas others cause infectious diseases in mammals. Some Pythium species can be used as biocontrol agents for plant diseases or mosquito management. Despite that phylogenetically close oomycete pathogens secrete RXLR effectors to enable infection, no RXLR protein was previously characterized in any Pythium species. Here we developed a stringent method to predict Pythium RXLR effectors and compared them with known RXLRs from other species. All oomycetous RXLRs form a huge superfamily, which indicates they may share a common ancestor. Our sequence analysis results suggest that the expansion of RXLR repertoire results from gene duplication and genome recombination events. We further demonstrated that most predicted Pythium RXLRs can be transcribed and some of them encode effectors exhibiting pathogenic or defense-inducing activities. This work expands our understanding of RXLR evolution in oomycetes in general, and provides novel insights into the molecular interactions between Pythium pathogens and their diverse hosts.

scholarly journals Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control Agent Trichogramma brassicae

2020 ◽  
Vol 10 (10) ◽  
pp. 3533-3540 ◽  
Author(s):  
Kim B. Ferguson ◽  
Tore Kursch-Metz ◽  
Eveline C. Verhulst ◽  
Bart A. Pannebakker
Keyword(s):  
Biological Control ◽  
De Novo ◽  
Biological Control Agent ◽  
Egg Parasitoid ◽  
Control Agent ◽  
Evidence Based ◽  
Trichogramma Brassicae ◽  
A Genome ◽  
Hybrid Genome ◽  
Essential Resource

Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

scholarly journals Hybrid genome assembly and evidence-based annotation of the egg parasitoid and biological control agent Trichogramma brassicae

2020 ◽  
Author(s):  
K. B. Ferguson ◽  
T. Kursch-Metz ◽  
E. C. Verhulst ◽  
B. A. Pannebakker
Keyword(s):  
Biological Control ◽  
De Novo ◽  
Biological Control Agent ◽  
Egg Parasitoid ◽  
Control Agent ◽  
Evidence Based ◽  
Trichogramma Brassicae ◽  
A Genome ◽  
Hybrid Genome ◽  
Essential Resource

ABSTRACTTrichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

scholarly journals De Novo Transcriptome Identifies Olfactory Genes in Diachasmimorpha longicaudata (Ashmead)

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 144 ◽  
Author(s):  
Liangde Tang ◽  
Jimin Liu ◽  
Lihui Liu ◽  
Yonghao Yu ◽  
Haiyan Zhao ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Control Agent ◽  
Odorant Receptor ◽  
Parasitoid Wasp ◽  
Control Agent ◽  
Fruit Flies ◽  
Ionotropic Receptor ◽  
Protein Levels ◽  
Diachasmimorpha Longicaudata ◽  
Sensory Neuron Membrane Protein

Diachasmimoorpha longicaudata (Ashmead, D. longicaudata) (Hymenoptera: Braconidae) is a solitary species of parasitoid wasp and widely used in integrated pest management (IPM) programs as a biological control agent in order to suppress tephritid fruit flies of economic importance. Although many studies have investigated the behaviors in the detection of their hosts, little is known of the molecular information of their chemosensory system. We assembled the first transcriptome of D. longgicaudata using transcriptome sequencing and identified 162,621 unigenes for the Ashmead insects in response to fruit flies fed with different fruits (guava, mango, and carambola). We annotated these transcripts on both the gene and protein levels by aligning them to databases (e.g., NR, NT, KEGG, GO, PFAM, UniProt/SwissProt) and prediction software (e.g., SignalP, RNAMMER, TMHMM Sever). CPC2 and MIREAP were used to predict the potential noncoding RNAs and microRNAs, respectively. Based on these annotations, we found 43, 69, 60, 689, 26 and 14 transcripts encoding odorant-binding protein (OBP), chemosensory proteins (CSPs), gustatory receptor (GR), odorant receptor (OR), odorant ionotropic receptor (IR), and sensory neuron membrane protein (SNMP), respectively. Sequence analysis identified the conserved six Cys in OBP sequences and phylogenetic analysis further supported the identification of OBPs and CSPs. Furthermore, 9 OBPs, 13 CSPs, 3 GRs, 4IRs, 25 ORs, and 4 SNMPs were differentially expressed in the insects in response to fruit flies with different scents. These results support that the olfactory genes of the parasitoid wasps were specifically expressed in response to their hosts with different scents. Our findings improve our understanding of the behaviors of insects in the detection of their hosts on the molecular level. More importantly, it provides a valuable resource for D. longicaudata research and will benefit the IPM programs and other researchers in this filed.

scholarly journals De novo assembly of the Pasteuria penetrans genome reveals high plasticity, host dependency, and BclA-like collagens

2018 ◽  
Author(s):  
Jamie N Orr ◽  
Tim H Mauchline ◽  
Peter J Cock ◽  
Vivian C Blok ◽  
Keith G Davies
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Biological Control Agent ◽  
Control Agent ◽  
Complete Sequence ◽  
Parasitic Nematodes ◽  
High Plasticity ◽  
Pasteuria Penetrans ◽  
Culture Methods

1.ABSTRACTPasteuria penetrans is a gram-positive endospore forming bacterial parasite of Meloidogyne spp. the most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic nature of P. penetrans makes it an attractive candidate biological control agent. However, deployment of P. penetrans for this purpose is inhibited by a lack of understanding of its metabolism and the molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium which makes obtaining genomic DNA of sufficient quantity and quality which is free from contamination challenging. Taking advantage of recent developments in whole genome amplification, long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate large quantities of high molecular weight genomic DNA from a small number of purified endospores. We demonstrate this method via genomic assembly of P. penetrans. This assembly reveals a reduced genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent expansion of transposases and prediction of partial competence pathways suggest a high degree of genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely related to Thermoactinomyces species. Seventeen predicted BclA-like proteins are identified which may be involved in the determination of attachment specificity. This resource may be used to develop in vitro culture methods and to investigate the genetic and molecular basis of attachment specificity.

De novo transcriptome analysis of the egg parasitoid Trichogramma chilonis Ishii (Hymenoptera: Trichogrammatidae): A biological control agent

Gene Reports ◽  
2018 ◽  
Vol 13 ◽  
pp. 115-129
Author(s):  
Ondara Zablon Kerima ◽  
Pathappa Niranjana ◽  
B.S. Vinay Kumar ◽  
Rajeshwari Ramachandrappa ◽  
Sharanappa Puttappa ◽  
...  
Keyword(s):  
Biological Control ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Biological Control Agent ◽  
Egg Parasitoid ◽  
Control Agent ◽  
De Novo Transcriptome ◽  
Trichogramma Chilonis

scholarly journals Growth and Maintenance of Wolbachia in Insect Cell Lines

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 706
Author(s):  
Ann M. Fallon
Keyword(s):  
Cell Lines ◽  
Insect Cell ◽  
Cultured Cells ◽  
Biological Control Agent ◽  
Wolbachia Infection ◽  
Control Agent ◽  
Host Cells ◽  
Gene Drive ◽  
Insect Cell Lines

The obligate intracellular microbe, Wolbachia pipientis (Rickettsiales; Anaplasmataceae), is a Gram-negative member of the alpha proteobacteria that infects arthropods and filarial worms. Although closely related to the genera Anaplasma and Ehrlichia, which include pathogens of humans, Wolbachia is uniquely associated with invertebrate hosts in the clade Ecdysozoa. Originally described in Culex pipiens mosquitoes, Wolbachia is currently represented by 17 supergroups and is believed to occur in half of all insect species. In mosquitoes, Wolbachia acts as a gene drive agent, with the potential to modify vector populations; in filarial worms, Wolbachia functions as a symbiont, and is a target for drug therapy. A small number of Wolbachia strains from supergroups A, B, and F have been maintained in insect cell lines, which are thought to provide a more permissive environment than the natural host. When transferred back to an insect host, Wolbachia produced in cultured cells are infectious and retain reproductive phenotypes. Here, I review applications of insect cell lines in Wolbachia research and describe conditions that facilitate Wolbachia infection and replication in naive host cells. Progress in manipulation of Wolbachia in vitro will enable genetic and biochemical advances that will facilitate eventual genetic engineering of this important biological control agent.

The effect of the hyperparasite (Gliocladium virens) on Rhizoctonia solani and on Rhizoctonia root rot of white beans

1981 ◽  
Vol 59 (1) ◽  
pp. 22-27 ◽  
Author(s):  
J. C. Tu ◽  
O. Vaartaja
Keyword(s):  
Rhizoctonia Solani ◽  
Root Rot ◽  
Biological Control Agent ◽  
Light And Electron Microscopy ◽  
Control Agent ◽  
Host Cells ◽  
Sequence Of Events ◽  
Rhizoctonia Root Rot ◽  
Gliocladium Virens

Using light and electron microscopy, Gliocladium virens is proved to be a hyperparasite of Rhizoctonia solani. When hyphae of G. virens come in contact with those of R. solani, the following sequence of events are observed (i) contact of G. virens with host cells, (ii) formation of appresoria, (iii) penetration of host cells, (iv) formation of intracellular hyphae, and (v) collapse and death of host cells. In vitro, G. virens effectively inhibited sclerotial formation of R. solani.Greenhouse tests showed that the presence of G. virens in soil artificially infested with R. solani reduced at planting the severity of Rhizoctonia root rot in white beans. Root rot severity decreased with increasing concentrations of G. virens. A similar result was obtained in soil treated with the two fungi 2 months prior to planting. This study suggests that G. virens may be a promising biological control agent for Rhizoctonia root rot of white beans.

scholarly journals Conserved RxLR Effectors From Oomycetes Hyaloperonospora arabidopsidis and Phytophthora sojae Suppress PAMP- and Effector-Triggered Immunity in Diverse Plants

2018 ◽  
Vol 31 (3) ◽  
pp. 374-385 ◽  
Author(s):  
Devdutta Deb ◽  
Ryan G. Anderson ◽  
Theresa How-Yew-Kin ◽  
Brett M. Tyler ◽  
John M. McDowell
Keyword(s):  
Plant Pathogens ◽  
Phytophthora Species ◽  
Phytophthora Sojae ◽  
Effector Proteins ◽  
Host Cells ◽  
Rxlr Effectors ◽  
Genes Encoding ◽  
Effector Triggered Immunity ◽  
Hyaloperonospora Arabidopsidis ◽  
Diverse Plant

Effector proteins are exported to the interior of host cells by diverse plant pathogens. Many oomycete pathogens maintain large families of candidate effector genes, encoding proteins with a secretory leader followed by an RxLR motif. Although most of these genes are very divergent between oomycete species, several genes are conserved between Phytophthora species and Hyaloperonospora arabidopsidis, suggesting that they play important roles in pathogenicity. We describe a pair of conserved effector candidates, HaRxL23 and PsAvh73, from H. arabidopsidis and P. sojae respectively. We show that HaRxL23 is expressed early during infection of Arabidopsis. HaRxL23 triggers an ecotype-specific defense response in Arabidopsis, suggesting that it is recognized by a host surveillance protein. HaRxL23 and PsAvh73 can suppress pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) in Nicotiana benthamiana and effector-triggered immunity (ETI) in soybean. Transgenic Arabidopsis constitutively expressing HaRxL23 or PsAvh73 exhibit suppression of PTI and enhancement of bacterial and oomycete virulence. Together, our experiments demonstrate that these conserved oomycete RxLR effectors suppress PTI and ETI across diverse plant species.

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