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Krait2: a versatile software for microsatellite investigation, visualization and marker development.
BMC Genomics
January 2025
Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610225, China.
Background: Microsatellites are highly polymorphic repeat sequences ubiquitously interspersed throughout almost all genomes which are widely used as powerful molecular markers in diverse fields. Microsatellite expansions play pivotal roles in gene expression regulation and are implicated in various neurological diseases and cancers. Although much effort has been devoted to developing efficient tools for microsatellite identification, there is still a lack of a powerful tool for large-scale microsatellite analysis.
View Article and Find Full Text PDFChromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies.
Sci Data
January 2025
Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon Tong, Hong Kong.
Black carp (Mylopharyngodon piceus) is one of the "four famous domestic fishes" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies.
View Article and Find Full Text PDFNatural variation of CTB5 confers cold adaptation in plateau japonica rice.
Nat Commun
January 2025
Frontiers Science Center for Molecular Design Breeding, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
During cold acclimation in high-latitude and high-altitude regions, japonica rice develops enhanced cold tolerance, but the underlying genetic basis remains unclear. Here, we identify CTB5, a homeodomain-leucine zipper (HD-Zip) transcription factor that confers cold tolerance at the booting stage in japonica rice. Four natural variations in the promoter and coding regions enhance cold response and transcriptional regulatory activity, enabling the favorable CTB5 allele to improve cold tolerance.
View Article and Find Full Text PDFEpigenetic variation in light of population genetic practice.
Nat Commun
January 2025
Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.
The evolutionary impact of epigenetic variation depends on its transgenerational stability and source - whether genetically determined, environmentally induced, or due to spontaneous, genotype-independent mutations. Here, we evaluate current approaches for investigating an independent role of epigenetics in evolution, pinpointing methodological challenges. We further identify opportunities arising from integrating epigenetic data with population genetic analyses in natural populations.
View Article and Find Full Text PDFAutomated scoring to assess RAD51-mediated homologous recombination in ovarian patient-derived tumor organoids.
Lab Invest
January 2025
Université de Caen Normandie, INSERM U1086 ANTICIPE, Caen, France; UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France; Université de Caen Normandie, US PLATON- ORGAPRED core facility, Caen, France; Université de Caen Normandie, US PLATON, UNICANCER, Comprehensive Cancer Center François Baclesse- Biological Resource Center 'OvaRessources', Caen, France. Electronic address:
PARP inhibitors (PARPi) have been shown to improve progression-free survival, particularly in homologous recombination deficient (HRD) ovarian cancers. Identifying patients eligible to PARPi is currently based on next-generation sequencing (NGS), but the persistence of genomic scars in tumors after restoration of HR or epigenetic changes can be a limitation. Functional assays could thus be used to improve this profiling and faithfully identify HRD tumors.
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