Full length sequencing reveals novel transcripts of detoxification genes along with related alternative splicing events and lncRNAs in Phyllotreta striolata

Shen, Guang Mao; Ou, Shi Yuan; He, Chu; Liu, Jie; He, Lin

doi:10.1371/journal.pone.0248749

Cited by 8 publications

(5 citation statements)

References 51 publications

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“…At present, the third-generation sequencing technology (e.g., PacBio SMRT) has greatly facilitated the de novo assembly of transcriptomes of many higher organisms and has helped to overcome the problems of short splicing and incomplete information for the species without reference genomes (Cheng et al, 2017 ; Chao et al, 2019 ; Kan et al, 2020 ; Shen et al, 2021 ). Meanwhile, second-generation sequencing (e.g., Illumina platform) has been widely used to obtain more comprehensive annotation information of many plant species (Yang et al, 2018 ; Luo et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L.

Song²,

Zhou³

et al. 2022

Front. Plant Sci.

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Bromus inermis L. (commonly known as smooth bromegrass) is a grass species with high nutritional value, great palatability, cold tolerance, and grazing resistance, which has been widely cultivated for pasture and sand fixation in northern and northwestern China. Salt stress is a main environmental factor limiting growth and production of smooth bromegrass. In this study, we performed PacBio Iso-Seq to construct the first full-length transcriptome database for smooth bromegrass under 300 mM NaCl treatment at different time points. Third-generation full-length transcriptome sequencing yielded 19.67 G polymerase read bases, which were assembled into 355,836 full-length transcripts with an average length of 2,542 bp. A total of 116,578 differentially expressed genes were obtained by comparing the results of third-generation sequencing and second-generation sequencing. GO and KEGG enrichment analyses revealed that multiple pathways were differently activated in leaves and roots. In particular, a number of genes participating in the molecular network of plant signal perception, signal transduction, transcription regulation, antioxidant defense, and ion regulation were affected by NaCl treatment. In particular, the CBL-CIPK, MAPK, ABA signaling network, and SOS core regulatory pathways of Ca2+ signal transduction were activated to regulate salt stress response. In addition, the expression patterns of 10 salt-responsive genes were validated by quantitative real-time PCR, which were consistent with those detected by RNA-Seq. Our results reveal the molecular regulation of smooth bromegrass in response to salt stress, which are important for further investigation of critical salt responsive genes and molecular breeding of salt-tolerant smooth bromegrass.

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Section: Discussionmentioning

confidence: 99%

Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L.

Song²,

Zhou³

et al. 2022

Front. Plant Sci.

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“…As a kind of detoxification enzyme, UGTs widely exist in lepidopteran insects, including B . mori ( Huang et al, 2008 ), S. litura and many other species ( Shen et al, 2021 ; Shi et al, 2019 ). In typical cases, UGTs are classified into two distinct subfamilies, UGT1 and UGT2.…”

Section: Discussionmentioning

confidence: 99%

“…All transcripts were functionally annotated based on the six databases, NCBI non-redundant protein sequences (NR) database using blastx with e-value <1e −5 ( Pruitt, Tatusova & Maglott, 2007 ), Protein family (Pfam) database using Hmmscan, a HMMER-based approach for detecting matches to Pfam families ( Finn, Clements & Eddy, 2011 ; Finn et al, 2009 ), a manually annotated and reviewed protein sequence (Swiss-Prot) database ( Bairoch & Apweiler, 2000 ), Clusters of Orthologous Groups of proteins (KOG) database ( Tatusov et al, 2000 ), Kyoto Encyclopedia of Genes and Genomes (KEGG) database using Diamond v0.8.36 software with e-value <1e −5 ( Kanehisa & Goto, 2000 ), Gene Ontology (GO) database using Blast2GO v2.5 ( Conesa et al, 2005 ; Consortium, 2004 ), individually. To identify alternative splicing events, transcripts were further processed using Astalavista software with default parameters ( Foissac & Sammeth, 2007 ), and we defined alternative splicing events based on the criteria of previous description ( Shen et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes

Yang

Xing

et al. 2021

PeerJ

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Background Spodoptera frugiperda (J. E. Smith), commonly known as fall armyworm (FAW), is one of the most destructive agricultural pests in the world and has posed a great threat to crops. The improper use of insecticides has led to rapid development of resistance. However, the genetic data available for uncovering the insecticide resistance mechanisms are scarce. Methods In this study, we used PacBio single-molecule real-time (SMRT) sequencing aimed at revealing the full-length transcriptome profiling of the FAW larval brain to obtain detoxification genes. Results A total of 18,642 high-quality transcripts were obtained with an average length of 2,371 bp, and 11,230 of which were successfully annotated in six public databases. Among these, 5,692 alternative splicing events were identified.

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“…In practice, the adults are preferred for control methods because the larvae are covert. However, the adults have a strong tolerance to chemical pesticides [ 5 ]. In China, there are approximately thirty pesticides (single and mixture) registered ( , accessed on 2 June 2023), but the most common insecticides such as organophosphorus, pyrethroids, and neonicotinoids only have a control efficacy of <85%, based on our evaluation (no published).…”

Section: Introductionmentioning

confidence: 99%

Screening of Fungal Strains and Formulations of Metarhizium anisopliae to Control Phyllotreta striolata in Chinese Flowering Cabbage

Chen

Wei

et al. 2023

Insects

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(1) Background: The cabbage flea beetle (CFB; Phyllotreta striolata) seriously damages the production of Chinese flowering cabbage (CFC; Brassica campestris L. ssp. chinensis var. utilis), which is a key leafy vegetable in South China. A large number of chemical insecticides have been sprayed to control this pest; as a result, residues and resistances are becoming an issue. It is necessary to develop biocontrol technologies to address this issue. (2) Methods: Fungal strains were selected based on bioactivity against CFB, and CFC seed pelletization with fungal conidia was subject to evaluation of control efficacy against CFB. The effective mixture of fungus and chemical insecticide was determined based on safety and joint toxicology tests. (3) Results: The screening of 103 strains from 14 genera identified the Metarhizium anisopliae strain MaGX19S02 (Ma) as the one with the highest virulence. The LC50s of Ma to CFB adult and second instar larvae on day 9 post-treatment were 3.04 × 106 and 27.2 × 106 spores/mL, respectively. In the pot test, the pelletization of CFC seeds with Ma conidia (50/25/12.5 mg in 1 g seed with 4 g fillers) demonstrated significant CFB mortalities (45–82%) 20 days after the larvae were introduced. In the field test, the seed pelletization achieved 57–81% control efficacy 14 days after sowing. Furthermore, the combination of Ma with chlorfenapyr (Chl) demonstrated a synergistic effect against CFB; based on this result, we prepared the mixture formulation of 20% Ma-Chl wettable powder (WP). The assessment of the effects of 20% Ma-Chl WP (500× diluent) against CFB revealed 93.33% mortality in the pot test and 61.3% control efficacy in the field test on day 7 post-treatment. (4) Conclusions: The findings demonstrate the potential of Ma to control CFB in the field. Seed pelletization with Ma conidia effectively controlled CFB larvae and protected CFC seedlings, wherein a mixture formulation of 20% Ma-Chl WP had substantial efficacy in controlling CFB adults. Our research provides new methods for CFB biocontrol.

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Full length sequencing reveals novel transcripts of detoxification genes along with related alternative splicing events and lncRNAs in Phyllotreta striolata

Cited by 8 publications

References 51 publications

Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L.

Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L.

Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes

Screening of Fungal Strains and Formulations of Metarhizium anisopliae to Control Phyllotreta striolata in Chinese Flowering Cabbage

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