Abstract:Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout … Show more
“…The virus sequences from the H. glycines PA3 population sequenced in this study are described by Ruark et al . 32 and the endosymbiont-associated transcripts were characterized in more detail as described below. Figure 1 Species distribution of predicted homologues to H. glycines .…”
Section: Resultsmentioning
confidence: 99%
“…In addition to a bacterial endosymbiont, several putative homologs from viruses were also identified. Previously, researchers found representative viruses from the Bornaviridae, Rhabdoviridae , and Bunyaviridae families contained within H. glycines 26 , 32 . Thus, there appears to be a significant microbial community active within H. glycines that has until now remained largely unexplored.…”
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
“…The virus sequences from the H. glycines PA3 population sequenced in this study are described by Ruark et al . 32 and the endosymbiont-associated transcripts were characterized in more detail as described below. Figure 1 Species distribution of predicted homologues to H. glycines .…”
Section: Resultsmentioning
confidence: 99%
“…In addition to a bacterial endosymbiont, several putative homologs from viruses were also identified. Previously, researchers found representative viruses from the Bornaviridae, Rhabdoviridae , and Bunyaviridae families contained within H. glycines 26 , 32 . Thus, there appears to be a significant microbial community active within H. glycines that has until now remained largely unexplored.…”
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
“…Nematode eggs maintained at the University of Missouri and juveniles maintained at Cornell University and North Carolina State University were collected similarly to the process described for RNAseq. The inbreeding protocol, date of origin, and HG type of SCN populations used for this manuscript can be viewed in a previous publication from our laboratory [ 7 ]. Total RNA was extracted as described previously via an adapted TRIzol ® Reagent protocol (Invitrogen, Carlsbad, CA) [ 14 ].…”
Section: Methodsmentioning
confidence: 99%
“…qRT-PCR was conducted to determine if the proposed viral genomes were detectable in nematode samples. The SCN-specific internal control genes GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) [ 7 ] and HgFAR1 ( H . glycines fatty acid and retinol binding protein-1) [ 5 ] were used to determine the relative quantification of viral titers.…”
Section: Methodsmentioning
confidence: 99%
“…Additionally, a novel nodavirus element has recently been described within the plant parasitic pinewood nematode, Bursaphelenchus xylophilus [ 6 ]. Previous research has demonstrated the widespread prevalence of the known SCN viruses within inbred and field populations as well as other Heterodera species including beet and clover cyst nematode [ 7 ]. In addition, we confirmed that these viruses replicate within the nematode host and are found in multiple life stages.…”
The study of invertebrate–and particularly nematode–viruses is emerging with the advancement of transcriptome sequencing. Five single-stranded RNA viruses have now been confirmed within the economically important soybean cyst nematode (SCN; Heterodera glycines). From previous research, we know these viruses to be widespread in greenhouse and field populations of SCN. Several of the SCN viruses were also confirmed within clover (H. trifolii) and beet (H. schachtii) cyst nematodes. In the presented study, we sequenced the transcriptomes of several inbred SCN populations and identified two previously undiscovered viral-like genomes. Both of these proposed viruses are negative-sense RNA viruses and have been named SCN nyami-like virus (NLV) and SCN bunya-like virus (BLV). Finally, we analyzed publicly available transcriptome data of two potato cyst nematode (PCN) species, Globodera pallida and G. rostochiensis. From these data, a third potential virus was discovered and called PCN picorna-like virus (PLV). PCN PLV is a positive-sense RNA virus, and to the best of our knowledge, is the first virus described within PCN. The presence of these novel viruses was confirmed via qRT-PCR, endpoint PCR, and Sanger sequencing with the exception of PCN PLV due to quarantine restrictions on the nematode host. While much work needs to be done to understand the biological and evolutionary significance of these viruses, they offer insight into nematode ecology and the possibility of novel nematode management strategies.
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