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Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves.
BMC Genomics
January 2025
The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages.
View Article and Find Full Text PDFComprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling.
Nucleic Acids Res
December 2024
MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
The ciliate Tetrahymena thermophila is a well-established unicellular model eukaryote, contributing significantly to foundational biological discoveries. Despite its acknowledged importance, current studies on Tetrahymena biology face challenges due to gene annotation inaccuracy, particularly the notable absence of untranslated regions (UTRs). To comprehensively annotate the Tetrahymena macronuclear genome, we collected extensive transcriptomic data spanning various cell stages.
View Article and Find Full Text PDFRepair of replication-dependent double-strand breaks differs between the leading and lagging strands.
Mol Cell
January 2025
Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address:
Single-strand breaks (SSBs) are one of the most commonly occurring endogenous lesions with the potential to give rise to cytotoxic double-strand breaks (DSBs) during DNA replication. To investigate how replication-dependent DSBs are repaired, we employed Cas9 nickase (nCas9) to generate site- and strand-specific nicks in the budding yeast genome. We found that nCas9-induced nicks are converted to mostly double-ended DSBs during S phase.
View Article and Find Full Text PDFDNA nicks in both leading and lagging strand templates can trigger break-induced replication.
Mol Cell
January 2025
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. Electronic address:
Article Synopsis
- Replication forks encountering unrepaired single-strand breaks (SSBs) can lead to both single-ended (seDSBs) and double-ended double-strand breaks (deDSBs), which are significant in cancer development.
- The study reveals that in fission yeast, SSBs typically result in deDSBs repaired by homologous recombination, but can also initiate break-induced replication (BIR).
- The occurrence of BIR is more frequent when DNA replication fork convergence is delayed and the Ku70 protein, involved in non-homologous end joining, is absent.
Comparative analysis of transcriptomics of Fasciola hepatica at different developmental stages.
Trop Biomed
September 2024
Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Diseases, Ministry of Agriculture, College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China.
This study explored the transcriptome differences in Fasciola hepatica at different developmental stages and identified functional genes related to growth and development during juvenile stages. DNBSEQ eukaryotic strand-specific transcriptome resequencing technology was used to sequence the transcriptomes of Fasciola hepatica eggs, juveniles, and adults. Additionally, the genes that were highly expressed during the juvenile stage were validated using qRT-PCR.
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