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Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control
Multiple aspects of mRNA translation are subject to regulation. Here we present a ribosome footprinting protocol to determine the location and...
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Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton
BackgroundThe epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the...
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Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves
Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding...
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Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
BackgroundThe cis-regulatory element became increasingly important for resistance breeding. There were many DNA variations identified by...
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Mechanism underlying the rapid growth of Phalaenopsis equestris induced by 60Co-γ-ray irradiation
Gamma (γ)-ray irradiation is one of the important modern breeding methods. Gamma-ray irradiation can affect the growth rate and other characteristics...
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‘Candidatus Phytoplasma mali’ SAP11-Like protein modulates expression of genes involved in energy production, photosynthesis, and defense in Nicotiana occidentalis leaves
Background‘ Candidatus Phytoplasma mali’, the causal agent of apple proliferation disease, exerts influence on its host plant through various...
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Comparative genomic investigation of TCP gene family in eggplant (Solanum melongena L.) and expression analysis under divergent treatments
Key messageThe putative TCP genes and their responses to abiotic stress in eggplant were comprehensively characterized, and SmTCP genes ( Smechr0202855.1...
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Genome-Wide Identification and Characterization of LIM Gene Family in Grapevine (Vitis vinifera L.) and Their Expression Analysis at Early Bud Developmental Stages
AbstractThe LIM gene (an acronym for Lin-11, Isl-1, and Mec-3 domain) is a transcription factor family widely distributed in plants. LIM proteins in...
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Identification of flowering genes in Camellia perpetua by comparative transcriptome analysis
Camellia perpetua has the excellent characteristic of flowering multiple times throughout the year, which is of great importance to solve the problem...
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The Chaperone Protein Cct5 is Essential for Hematopoietic Stem Cell Maintenance
Proper proteostasis is indispensable for the long-term maintenance of hematopoietic stem and progenitor cells (HSPCs). The TRiC/CCT...
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Comparative physiological, biochemical, metabolomic, and transcriptomic analyses reveal the formation mechanism of heartwood for Acacia melanoxylon
Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and...
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ORFik: a comprehensive R toolkit for the analysis of translation
BackgroundWith the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics,...
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Genome-Wide Identification and Comprehensive Analyses of TCP Gene Family in Banana (Musa L.)
Teosinte Branched, Cycloidea, Proliferating Cell Factor proteins are a large family of transcription factors in angiosperms and are specific for each...
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The Acer palmatum TCP Transcription Factor ApTCP2 Controls Leaf Morphogenesis, Accelerates Senescence, and Affects Flowering via miR319 in Arabidopsis thaliana
TCP transcription factors are important regulators of plant growth and proliferation processes, such as leaf morphogenesis, petal growth and...
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Characterization and analysis of the transcriptome response to drought in Larix kaempferi using PacBio full-length cDNA sequencing integrated with de novo RNA-seq reads
Main conclusionA hypothetical model of drought tolerance mechanism of Larix kaempferi was established through SMRT-seq and Illumina HiSeq.
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Principles, challenges, and advances in ribosome profiling: from bulk to low-input and single-cell analysis
Ribosome profiling has revolutionized our understanding of gene expression regulation by providing a snapshot of global translation in vivo. This...
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Regulatory dynamics of gene expression in the develo** male gametophyte of Arabidopsis
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands...
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Transcriptome analysis and functional validation reveal the novel role of LhCYCL in axillary bud development in hybrid Liriodendron
Shoot branching significantly influences yield and timber quality in woody plants, with hybrid Liriodendron being particularly valuable due to its...
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HB31 and HB21 regulate floral architecture through miRNA396/GRF modules in Arabidopsis
Floral architecture plays a pivotal role in developmental processes under genetic regulation and is also influenced by environmental cues. This...
