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First genome-specific development, characterization and validation of simple sequence repeat (SSR) markers in , a commercially important bamboo of India.
3 Biotech
February 2025
Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, Uttarakhand 248195 India.
The natural population of have not been genetically enumerated due to a lack of genome sequence information or robust species-specific molecular marker. The present study was conducted to develop and validate genome-wide de novo simple sequence repeat (SSRs) markers in through shallow-pass genome sequencing. The genome sequence data of about 13 Gb was generated using Illumina technology, and high-quality sequence reads were de novo assembled into 1,390,995 contigs with GC content 42.
View Article and Find Full Text PDFFRET analysis of the unwrapping of nucleosomal DNA containing a sequence characteristic of the + 1 nucleosome.
Sci Rep
January 2025
Molecular Modeling and Simulation Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1, Anagawa, Inage-Ku, Chiba City, Chiba, 263-8555, Japan.
Sequence-dependent mechanical properties of DNA could play essential roles in nuclear processes by affecting histone-DNA interactions. Previously, we found that the DNA entry site of the first nucleosomes from the transcription start site (+ 1 nucleosome) in budding yeast enriches AA/TT steps, but not the exit site, and the biased presence of AA/TT in the entry site was associated with the transcription levels of yeast genes. Because AA/TT is a rigid dinucleotide step, we considered that AA/TT causes DNA unwrapping.
View Article and Find Full Text PDFDevelopment of Roselle ( L.) Transcriptome-Based Simple Sequence Repeat Markers and Their Application in Roselle.
Plants (Basel)
December 2024
Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Roselle ( L.) simple sequence repeat (SSR) markers were developed using RNA sequencing technology, providing a foundation for genetic analysis and the identification of roselle varieties. In this study, 10 785 unigenes containing 12 994 SSR loci with an average of one SSR locus per 6.
View Article and Find Full Text PDFGenome-Wide In Silico Analysis of Microsatellite Loci in Rabbits.
Animals (Basel)
December 2024
Department of Poultry Breeding, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt.
This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences.
View Article and Find Full Text PDFGenomic microsatellite characterization and development of polymorphic microsatellites in Eospalax baileyi.
Sci Rep
January 2025
Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural College, Gansu Agricultural University, Lanzhou, 730070, China.
Microsatellite markers are cost-effective, rapid, efficient, and show great advantages in in large-sample kinship analysis and population structure studies. However, microsatellite loci are seriously underdeveloped in non-model organisms. The plateau zokor (Eospalax baileyi) is a key species living underground in the Tibetan Plateau, the effective management of which has long been challenging.
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