Identification of LincRNA from Dermatophagoides farinae (Acari: Pyroglyphidae) for Potential Allergen-Related Targets

Zhou, Ying; Wu, Mei‐Li; Zhu, Hanting; Shao, Junjie; Liu, Chang; Cui, Yubao

doi:10.1590/1678-4685-gmb-2019-0243

Cited by 2 publications

(2 citation statements)

References 17 publications

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“…lncRNA expression in the biological processes of development have been examined in insects [7,9]. In the mites, lncRNA has been identified in many physiological processes of mites such as V. destructor [33], T. cinnabarinus [34], and Dermatophagoides farina [36]. However, there is no previous report on the lncRNA involved in mite development and molting.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

Liu

Smagghe

et al. 2021

IJMS

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Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological strategy results in the short lifecycle of spider mites and difficulties in their control in the field. Long non-coding RNAs (lncRNAs) regulate transcriptional editing, cellular function, and biological processes. Thus, analysis of the lncRNAs in the spider mite molting process may provide new insights into their roles in the molting mechanism. For this purpose, we used high-throughput RNA-seq to examine the expression dynamics of lncRNAs and mRNAs in the molting process of different development stages in Panonychus citri. We identified 9199 lncRNAs from 18 transcriptomes. Analysis of the lncRNAs suggested that they were shorter and had fewer exons and transcripts than mRNAs. Among these, 356 lncRNAs were differentially expressed during three molting processes: late larva to early protonymph, late protonymph to early deutonymph, and late deutonymph to early adult. A time series profile analysis of differentially expressed lncRNAs showed that 77 lncRNAs were clustered into two dynamic expression profiles (Pattern a and Pattern c), implying that lncRNAs were involved in the molting process of spider mites. Furthermore, the lncRNA–mRNA co-expression networks showed that several differentially expressed hub lncRNAs were predicted to be functionally associated with typical molting-related proteins, such as cuticle protein and chitin biosynthesis. These data reveal the potential regulatory function of lncRNAs in the molting process and provide datasets for further analysis of lncRNAs and mRNAs in spider mites.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

Liu

Smagghe

et al. 2021

IJMS

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“…The library was submitted for quality control on the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR system and then sequenced on the Illumina HiSeq 2000 instrument to produce paired-end 2 × 100 bp reads, according to the vendor's recommended protocol. Sequencing data were pretreated, assembled, and annotated as described in our previous publications [ 36 , 37 ].…”

Section: Methodsmentioning

confidence: 99%

A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species

Hu,

Huang,

Zhou

et al. 2024

International Journal of Genomics

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Background. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods. We achieved a chromosome-level assembly of D. farinae’s genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. Results. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. Conclusion. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies.

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Identification of LincRNA from Dermatophagoides farinae (Acari: Pyroglyphidae) for Potential Allergen-Related Targets

Cited by 2 publications

References 17 publications

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri

A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species

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