ArticleMolecular plant pathology2018
Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae.
Article in Molecular plant pathology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 49 citations in OpenAlex.
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- Identification and Functions of lncRNAs in Fungi.Non-coding RNA · 2025Review
- Genome-wide identification of long non-coding RNAs reveals potential association withMicrobiology spectrum · 2025Article
- Correlation Between Effector Gene Expression Targeted by lncRNAs in the Oomycete Fish Pathogen, Saprolegnia parasitica.Marine biotechnology (New York, N.Y.) · 2024Article
- Underground communication: Long non-coding RNA signaling in the plant rhizosphere.Plant communications · 2024Review
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- Study on the Applications and Regulatory Mechanisms of Grafting on Vegetables.Plants (Basel, Switzerland) · 2023Review
- Identification of Long Intergenic Noncoding RNAs inMicrobiology spectrum · 2023Article
- Roles of long non-coding RNAs in plant immunity.PLoS pathogens · 2023Review
- The SET domain protein PsKMT3 regulates histone H3K36 trimethylation and modulates effector gene expression in the soybean pathogen Phytophthora sojae.Molecular plant pathology · 2023Article
- High-throughput time series expression profiling of Plasmopara halstedii infecting Helianthus annuus reveals conserved sequence motifs upstream of co-expressed genes.BMC genomics · 2023Article
- Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation.International journal of molecular sciences · 2023Article
- Genome-wide identification and characterization ofFrontiers in plant science · 2023Article
- Multi-Omics Techniques for Soybean Molecular Breeding.International journal of molecular sciences · 2022Review
- Function identification of miR394 in tomato resistance to Phytophthora infestans.Plant cell reports · 2021Article
- Secretory Peptides as Bullets: Effector Peptides from Pathogens against Antimicrobial Peptides from Soybean.International journal of molecular sciences · 2020Review
- Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens.Frontiers in microbiology · 2020Article
- Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution ofFrontiers in microbiology · 2019Article
- Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response inFrontiers in microbiology · 2019Article
- Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi.International journal of genomics · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.
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