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Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly.

ABSTRACT: Wheat Stem Sawfly (WSS), Cephus Cinctus Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant's resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regulatory functions on gene expression, tuning protein production by controlling transcriptional and post-transcriptional activities. A transcriptome-guided approach was followed in order to identify miRNAs, lncRNAs, and mRNA of WSS, and their interaction networks. A total of 1,893 were presented here as differentially expressed between larva and adult WSS insects. There were 11 miRNA families detected in WSS transcriptome. Together with the annotation of 1,251 novel mRNAs, the amount of genetic information available for WSS was expanded. The network between WSS miRNAs, lncRNAs, and mRNAs suggested miRNA-mediated regulatory roles of lncRNAs as competing endogenous RNAs. In the light of the previous evidence that small RNA molecules of a pathogen could suppress the immune response of host plant, we analyzed the putative interactions between larvae and wheat at the miRNA level. Overall, this study provides a profile of larva and adult WSS life stages in terms of coding and non-coding elements. These findings also emphasize the potential roles of wheat and larval miRNAs in wheat resistance to infestation and in the suppression of resistance which is critical for the development of effective pest control strategies.

SUBMITTER: Cagirici HB

PROVIDER: S-EPMC5630980 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly.

Cagirici Halise B HB Biyiklioglu Sezgi S Budak Hikmet H

Frontiers in plant science 20170926

Wheat Stem Sawfly (WSS), <i>Cephus Cinctus</i> Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant's resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regula ...[more]

PMID: 29038661

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Project description:The wheat stem sawfly (WSS), Cephus cinctus Norton, is an important wheat pest in the Northern Great Plains of the USA. No single control measure effectively suppresses WSS damage. This study provides information on the effects on the WSS adult settling preference behavior on wheat plants under laboratory conditions from treatment with both synthetic plant defense elicitors (Actigard® and cis-jasmone) and a botanical insecticide (Azadirachtin®). In addition, field experiments were performed to determine whether these chemicals impact the WSS fitness (larval mortality and larval body weight), winter wheat plant fitness (infestation, stem lodging, yield, and quality), adult population of WSS and Bracon spp., and larval parasitism levels. Our lab results showed that there were no significant differences in adult settling behavior on plants exposed separately to each chemical and control. In contrast, when adults were exposed simultaneously to treated and untreated plants, there was a significant reduction in the percentage of adults settling on Actigard® and Azadirachtin® treated plants compared to plants sprayed with water in the same cage. However, in field situations, regardless of application timing and field location, none of the chemicals significantly reduced adult population or stems damage. The exception was two times applications of Actigard® had significantly lower WSS infested stem damage levels at 30 days after initial treatment applications at Knees and 50 days at Choteau locations compared to control, but without effect at the Conrad location. The field study indicated that two times applications of Actigard® significantly increased diapausing larval mortality percentages and lowered stem lodging levels compared to untreated controls at Knees and Choteau locations, while no effects at Conrad location. Larval body weight was significantly lower in plots treated with Actigard® at Knees and Conrad, but no effects at Choteau. No significant differences were found in wheat yield and quality in plots treated with chemicals and controls at any location. Bracon spp. adult population and parasitism levels were not negatively affected by the use of chemicals. In conclusion, this study offers insights on what treatments should be emphasized in more detail despite variable findings.

Project description:BACKGROUND:Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. RESULTS:We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371?bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638?bp and 354?bp, respectively. Functional annotation was performed using NCBI's BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. CONCLUSIONS:We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S. lycopersicum, S. tuberosum, Capsicum spp, S. melongena and Petunia spp.

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Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly.

Publications

Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly.

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