Scirpophaga incertulas isolate:IIRRYSB17
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA558851 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15969031_1.fastq.gz | Fastqsanger.gz | |||
| SRR15969031_2.fastq.gz | Fastqsanger.gz | |||
| SRR15969032_1.fastq.gz | Fastqsanger.gz | |||
| SRR15969032_2.fastq.gz | Fastqsanger.gz |
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Project description:The yellow stem borer Scirpophaga incertulas is the dominant pest of rice in tropical Asia. However, the lack of genomic resources makes it difficult to understand their invasiveness and ecological adaptation. A high-quality chromosome-level genome of S. incertulas, a monophagous rice pest, was assembled by combining Illumina short reads, PacBio HiFi long sequencing, and Hi-C scaffolding technology. The final genome size was 695.65 Mb, with a scaffold N50 of 28.02 Mb, and 93.50% of the assembled sequences were anchored to 22 chromosomes. BUSCO analysis demonstrated that this genome assembly had a high level of completeness, with 97.65% gene coverage. A total of 14,850 protein-coding genes and 366.98 Mb of transposable elements were identified. In addition, comparative genomic analyses indicated that chemosensory processes and detoxification capacity may play critical roles in the specialized host preference of S. incertulas. In summary, the chromosome-level genome assembly of S. incertulas provides a valuable genetic resource for understanding the biological characteristics of its invasiveness and developing an efficient management strategy.
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Project description:The yellow stemborer, Scirpophaga incertulas, is a monophagous pest of rice, attacking the crop from its vegetative to reproductive stages. Microorganisms are crucial in influencing the insect's life cycle, evolution, and ecology, presenting an avenue for understanding and improving management strategies. Present research employed advanced next-generation sequencing technology to investigate the microbiota of S. incertulas, a previously unexplored area for developmental stage associated microbial diversity. The study used 16 S rRNA V3-V4 region amplicon sequencing to determine the diversity of bacteria associated with different developmental stages of S. incertulas. Taxonomically, bacterial communities were classified into 25 phyla, encompassing 46 classes, 101 orders, 197 families, and 364 genera. The major phyla identified were Proteobacteria (39%), Firmicutes (39%), Actinobacteria (11%), and Bacteroidetes (7%), with Proteobacteria being the most predominant across all developmental stages except the larval stage, where Firmicutes took precedence. Moraxellaceae, Bacillaceae, Xanthomonadaceae, Sphingobacteriaceae, and Flavobacteriaceae were predominant families across all the developmental stages. However, in the egg and adult stages, the abundance of Bacillaceae was notably lower, whereas Prevotellaceae found significantly higher in adult stages. Dominant genera across all stages included Acinetobacter, Bacillus, Lactobacillus, Enterococcus, and Pseudomonas. The result showed that the highest number of Operational Taxonomic Units (OTUs) were in the larval stage (426 OTUs), the lowest in adults (251 OTUs), and the egg stage (254 OTUs). This suggests that the microbiota may play a role in the growth and development of S. incertulas. The predicted functional assessment of the associated S. incertulas microbiota revealed that the microbiota primarily participated in metabolic pathways, secondary metabolite biosynthesis, energy metabolism, signaling, and cellular processes. Our findings shed light on the significant variations in the microbial community and their predicted functions present in S. incertulas across developmental stages. The present study findings will help in developing novel microbiota-based management strategies.
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Project description:The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.
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Project description:Rice yellow stem borer, Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae) is a serious pest, that causes significant yield loss (10-40%) to rice crop in India and other parts of the world. This study emphasizes the prediction of the potential invasion risk, distribution, and further spread of S. incertulas during current and future climate change scenarios in India and the world. The pest identity was confirmed with morphological taxonomy, and the possible habitat distribution and further spread in future climate scenarios were modelled using the MaxEnt algorithm. The climate niche for S. incertulas was also established by analyzing the correlation between the pest occurrence data of 143 locations in India and seven bioclimatic variables viz., bio01, bio02, bio03, bio05, bio12, bio13, and bio15, were chosen for predicting the distribution of S. incertulas. The model performance was good as it exhibited a strong Receiver Operating Characteristic Curve value of 0.949. Based on the Jackknife test, the Bio 13 (precipitation of the wettest month), exhibited the highest gain value and emerged as the primary abiotic factor exerting influence on the potential habitat distribution of this borer. The study demonstrated that bioclimatic variables annual mean temperature (30 °C), and annual precipitation (10-700 mm) favour its multiplication, infestation, and further spread to new areas. As the anticipated habitat range of S. incertulas is of considerable importance for researchers and other stakeholders involved in plant protection, the data generated here may be useful for researchers, policymakers, and farmers for designing better management strategies to mitigate this pest and curtail its spread to new rice growing areas in a rapidly changing global environment.
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