Articles

Identification and expression analysis of CCCH gene family and screening of key low temperature stress response gene CbuC3H24 and CbuC3H58 in Catalpa bungei

Catalpa bungei, a tree indigenous to China, is renowned for its superior timber quality and as an ornamental in horticulture. To promote the cultivation of C. bungei in cold regions and expand its distribution, e...

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Utility analyses of AVITI sequencing chemistry

DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and tran...

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Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon

Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretio...

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A transcription factor of SHI family AaSHI1 activates artemisinin biosynthesis genes in Artemisia annua

Transcription factors (TFs) of plant-specific SHORT INTERNODES (SHI) family play a significant role in regulating development and metabolism in plants. In Artemisia annua, various TFs from different families have...

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Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development

Appropriate regulation of genes expressed in oocytes and embryos is essential for acquisition of developmental competence in mammals. Here, we hypothesized that several genes expressed in oocytes and pre-impla...

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Characterization of a novel multi-resistant Pseudomonas juntendi strain from China with chromosomal bla_VIM−2 and a megaplasmid coharboring bla_{IMP−1−like} and bla_OXA−1

Pseudomonas juntendi is a newly identified opportunistic pathogen, of which we have limited understanding. P. juntendi strains are often multidrug resistant, which complicates clinical management of infection.

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Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant

Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effec...

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Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies

The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressu...

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The effect of acute social isolation on neural molecular responses in components of the social decision-making network

Prolonged or chronic social isolation has pronounced effects on animals, ranging from altered stress responses, increased anxiety and aggressive behaviour, and even increased mortality. The effects of shorter ...

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The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus

The harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, w...

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Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis

The Synotis (C. B. Clarke) C. Jeffrey & Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphologi...

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Correction: Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

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Canine hyper-sociability structural variants associated with altered three-dimensional chromatin state

Strong selection on complex traits can lead to skewed trait means and reduced trait variability in populations. An example of this phenomenon can be evidenced in allele frequency changes and skewed trait distr...

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Sex, tissue, and mitochondrial interactions modify the transcriptional response to rapamycin in Drosophila

Many common diseases exhibit uncontrolled mTOR signaling, prompting considerable interest in the therapeutic potential of mTOR inhibitors, such as rapamycin, to treat a range of conditions, including cancer, a...

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Identification of the effects of alkalinity exposure on the gills of oriental river prawns, Macrobrachium nipponense

Macrobrachium nipponense is an important commercial freshwater species in China. However, the ability of alkali tolerance of M. nipponense is insufficient to culture in the major saline-alkali water source in Chi...

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Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology

Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptor...

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Integrated transcriptome and metabolism unravel critical roles of carbon metabolism and oxidoreductase in mushroom with Korshinsk peashrub substrates

Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despit...

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Extensive differential DNA methylation between tuberculosis skin test positive and skin test negative cattle

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), represents a significant problem for the agriculture industry as well as posing a risk for human health. Current diagnostic tests for bTB targe...

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Convergent dwarfism consequences of minipigs under independent artificial selections

Currently, diverse minipigs have acquired a common dwarfism phenotype through independent artificial selections. Characterizing the population and genetic diversity in minipigs is important to unveil genetic m...

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Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India

In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discer...

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Integrated metabolomic and transcriptomic analysis reveals biosynthesis mechanism of flavone and caffeoylquinic acid in chrysanthemum

Chrysanthemum morifolium ‘HangBaiJu’, a popular medicinal and edible plant, exerts its biological activities primarily through the presence of flavones and caffeoylquinic acids (CQAs). However, the regulatory mec...

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Genome-wide identification and molecular evolution of elongation family of very long chain fatty acids proteins in Cyrtotrachelus buqueti

To reveal the molecular function of elongation family of very long chain fatty acids(ELO) protein in Cyrtotrachelus buqueti, we have identified 15 ELO proteins from C.buqueti genome. 15 CbuELO proteins were locat...

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Spatial transcriptome reveals the region-specific genes and pathways regulated by Satb2 in neocortical development

It is known that the neurodevelopmental disorder associated gene, Satb2, plays important roles in determining the upper layer neuron specification. However, it is not well known how this gene regulates other neoc...

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PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model

Long non-coding RNAs (lncRNAs) are RNA transcripts of more than 200 nucleotides that do not encode canonical proteins. Their biological structure is similar to messenger RNAs (mRNAs). To distinguish between ln...

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The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes

China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic...

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Genetic diversity, demographic history, and selective signatures of Silkie chicken

Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall ...

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Effect of enhanced plane of nutrition in early life on the transcriptome and proteome of the anterior pituitary gland in Angus heifer calves

Enhanced nutrition during the early calfhood period has been shown to lead to earlier pubertal development in heifer calves. This is of interest as earlier pubertal onset can subsequently facilitate earlier ca...

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Analysis of the recombination and evolution of the new type mutant pseudorabies virus XJ5 in China

Pseudorabies have caused enormous economic losses in China’s pig industry and have recurred on many large pig farms since late 2011. The disease is caused by highly pathogenic, antigenic variant pseudorabies v...

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Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high pr...

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RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs

Association testing between molecular phenotypes and genomic variants can help to understand how genotype affects phenotype. RNA sequencing provides access to molecular phenotypes such as gene expression and a...

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Genome-wide analysis of the PYL-PP2C-SnRK2s family in the ABA signaling pathway of pitaya reveals its expression profiles under canker disease stress

Abscisic acid (ABA) plays a crucial role in seed dormancy, germination, and growth, as well as in regulating plant responses to environmental stresses during plant growth and development. However, detailed inf...

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Characterization, evolution, and abiotic stress responses of leucine-rich repeat receptor-like protein kinases (LRR-RLK) in Liriodendron chinense

Liriodendron chinense is susceptible to extinction due to the increasing severity of abiotic stresses resulting from global climate change, consequently impacting its growth, development, and geographic distribut...

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Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade

Organellar genomes have become increasingly essential for studying genetic diversity, phylogenetics, and evolutionary histories of seaweeds. The order Dictyotales (Dictyotophycidae), a highly diverse lineage w...

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Genome assembly of redclaw crayfish (Cherax quadricarinatus) provides insights into its immune adaptation and hypoxia tolerance

The introduction of non-native species is a primary driver of biodiversity loss in freshwater ecosystems. The redclaw crayfish (Cherax quadricarinatus) is a freshwater species that exhibits tolerance to hypoxic s...

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Correction: HiFi long-read amplicon sequencing for full-spectrum variants of human mtDNA

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The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution

Mitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal proper...

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siqRNA-seq is a spike-in-independent technique for quantitative mapping of mRNA landscape

RNA sequencing (RNA-seq) is widely used for gene expression profiling and quantification. Quantitative RNA sequencing usually requires cell counting and spike-in, which is not always applicable to many samples...

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Bacillus anthracis in South Africa, 1975–2013: are some lineages vanishing?

The anthrax-causing bacterium Bacillus anthracis comprises the genetic clades A, B, and C. In the northernmost part (Pafuri) of Kruger National Park (KNP), South Africa, both the common A and rare B strains clade...

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Comparing methylation levels assayed in GC-rich regions with current and emerging methods

DNA methylation is an epigenetic mechanism that regulates gene expression, and for mammals typically occurs on cytosines within CpG dinucleotides. A significant challenge for methylation detection methods is a...

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Comparative transcriptome analysis reveals the impact of daily temperature difference on male sterility in photo-thermo-sensitive male sterile wheat

Photo-thermo-sensitive male sterility (PTMS), which refers to the male sterility triggered by variations in photoperiod and temperature, is a crucial element in the wheat two-line hybrid system. The developmen...

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Genome-wide association studies of body size traits in Tibetan sheep

Elucidating the genetic variation underlying phenotypic diversity will facilitate improving production performance in livestock species. The Tibetan sheep breed in China holds significant historical importance...

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Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population

The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this stud...

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SGK1 promotes the lipid accumulation via regulating the transcriptional activity of FOXO1 in bovine

Serum/glucocorticoid-inducible kinase 1 (SGK1) gene encodes a serine/threonine protein kinase that plays an essential role in cellular stress response and regulation of multiple metabolic processes. However, its ...

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Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis

Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, geneti...

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Transcriptome and weighted gene co-expression network analyses reveal key genes and pathways involved in early fruit ripening in Citrus sinensis

The fruit ripening period is an important target trait in fruit tree crop breeding programs. Thus, citrus tree breeders seek to develop extreme early ripening cultivars that allow optimization of citrus matura...

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The lactococcal ICE-ome encodes a repertoire of exchangeable traits with potential industrial relevance

Dairy industries apply selected lactococcal strains and mixed cultures to produce diverse fermented products with distinctive flavor and texture properties. Innovation of the starter culture functionality in c...

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Integrated analysis of transcriptomics and defense-related phytohormones to discover hub genes conferring maize Gibberella ear rot caused by Fusarium Graminearum

Gibberella ear rot (GER) is one of the most devastating diseases in maize growing areas, which directly reduces grain yield and quality. However, the underlying defense response of maize to pathogens infection...

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guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel

Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative....

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Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing...

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