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SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions
BackgroundTandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs...
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Predicted roles of long non-coding RNAs in abiotic stress tolerance responses of plants
The plant genome exhibits a significant amount of transcriptional activity, with most of the resulting transcripts lacking protein-coding potential....
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Distinguishing Puccinia striiformis f. sp. tritici Isolates Using Genomic Sequencing: A Case Study
We are reporting on the utilization of high-throughput sequencing and different sequencing analysis tools to delineate identification of different...
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Tissue and regional expression patterns of dicistronic tRNA–mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants
Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic...
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Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional variability
BackgroundCD-1 is an outbred mouse stock that is frequently used in toxicology, pharmacology, and fundamental biomedical research. Although inbred...
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A super-pangenome of the North American wild grape species
BackgroundCapturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic...
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The dicot homolog of maize PPR103 carries a C-terminal DYW domain and may have a role in C-to-U editing of some chloroplast RNA transcripts
In plants, cytidine-to-uridine (C-to-U) editing is a crucial step in processing mitochondria- and chloroplast-encoded transcripts. This editing...
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Rnf1 is the primary electron source to nitrogenase in a high-ammonium-accumulating strain of Azotobacter vinelandii
AbstractThe enzyme nitrogenase performs the process of biological nitrogen fixation (BNF), converting atmospheric dinitrogen gas into the...
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Nuclear lamina component KAKU4 regulates chromatin states and transcriptional regulation in the Arabidopsis genome
BackgroundThe nuclear lamina links the nuclear membrane to chromosomes and plays a crucial role in regulating chromatin states and gene expression....
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Nature of Genomic Architecture: A Topological Model of Genome
Our present understanding of genomic architecture is based on incremental addition of the manner in which genes are expressed. At present, there is...
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Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato
Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin...
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The Pathogen: Plasmodiophora brassicae
The pathogen Plasmodiophora brassicae Woronin is a very serious soil borne, intracellular, obligate, non-axenic, endoparasitic, wide spread, and...
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A foundational large language model for edible plant genomes
Significant progress has been made in the field of plant genomics, as demonstrated by the increased use of high-throughput methodologies that enable...
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Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study
Key messageNovel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with...
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Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences
BackgroundThe adaptive immune system of vertebrates has an extraordinary potential to sense and neutralize foreign antigens entering the body. De novo ...
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A newly discovered subtidal population of Undaria pinnatifida was determined not to be founded recently by the zoospores discharged from a nearby hatchery
Dalian is the most important farming region in China for the economically important kelp Undaria pinnatifida and there are several major hatcheries...
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Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed...
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Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes
BackgroundOur understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous...
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Molecular Markers in Pteridophytes
Identification and classification of lifeforms is an elementary step in knowledge generation and biodiversity management. Traditionally, taxonomical...
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Gene–allele system of shade tolerance in southern China soybean germplasm revealed by genome-wide association study using gene–allele sequence as markers
Key messageFifty-three shade tolerance genes with 281 alleles in the SCSGP were identified directly using gene–allele sequence as markers in RTM...
