Articles

Whole genome insights into genetic diversity, introgression, and adaptation of Yunnan indigenous cattle of Southwestern China

Yunnan Province, located in Southwestern China, the intricate geography, variable climate, and abundant vegetation of the region have collectively contributed to shaping the distinctive germplasm characteristi...

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Dissecting genomes of multiple yak populations: unveiling ancestry and high-altitude adaptation through whole-genome resequencing analysis

The present study was undertaken to elucidate the population structure and differentiation of Indian yak from Chinese and wild cohorts on genome-wide scale by identifying the selection sweeps and genomic basis...

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Analysis of the CRK expressions in bottle gourd (Lagenaria siceraria) under Fusarium oxysporum f. sp. lagenariae stress by using genome-wide identification strategy

The cysteine-rich receptor-like kinases (CRKs) family in plants have been reported to perform multiple functions against various stresses. However, the CRK family in bottle gourd (Lagenaria siceraria) has not bee...

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Integrated multiomic profiling of tail adipose tissue highlights novel genes, lipids, and metabolites involved in tail fat deposition in sheep

Tail fat is important for fat-tailed or fat-rumped sheep to survive in harsh environments. However, the molecular mechanism underlying tail fat deposition in sheep remains unclear. In this study, we comprehens...

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Characterization of avian β-defensin genes in Galliformes reveals widespread evolutionary diversification and distinct evolutionary relationships with infection risk

Avian β-defensins (AvBDs) represent a key family of antimicrobial host defense peptides in birds. Accumulating evidence suggests that the evolutionary trajectory of β-defensin genes is specific to the gene, ti...

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Assessing the association between ADH5 and ALDH1A1 genetic variants and substance use disorder risk in a Jordanian male population

Substance Use Disorder (SUD) is a severe global problem that is influenced by both environmental and genetic factors. The genetic etiology of addiction can be complex and overlapping. This study aimed to inves...

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Distribution and phylogenetic analysis of porcine parvoviruses in the wild boar population of Russia

Porcine parvoviruses (PPVs) are widespread worldwide in the swine population. PPV1 is a significant infectious agent in pig production, causing porcine reproductive failure. The pathogenic potential of novel P...

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Transcriptome analyses for revealing leaf abscission of Cyclocarya paliurus stem segments in vitro

Leaf abscission of Cyclocarya paliurus stem segments in vitro is very serious, and more than 90% of the leaves gradually fall off with prolonged culture time, which hinders breeding. This study investigated the m...

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Identification and analysis of miRNA - mRNA regulatory modules associated with resistance to bacterial leaf streak in rice

acterial leaf streak (BLS) is a bacterial disease that severely affects rice leaves, leading to significant yield reductions. microRNAs (miRNAs) are short non-coding RNAs extensively involved in the growth, de...

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Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds

Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within ...

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The effect of induced molting on the testicular physiological remodeling in no-semen roosters

The fertility of roosters significantly impacts the economic outcome of the poultry industry. However, it is common for some roosters to fail to produce semen during production, and the underlying reasons rema...

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Transcriptomic and biometric parameters analysis in rainbow trout (Oncorhynchus mykiss) challenged with viral hemorrhagic septicemia virus (VHSV)

Viral hemorrhagic septicemia virus (VHSV) is a highly pathogenic virus that poses a significant threat to the health of diverse marine species. Among these, trout species, particularly rainbow trout (Oncorhynchus...

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Comparative genomics uncovers evolutionary drivers of locust migratory adaptation

Locust migration is one of the main causes of locust plagues. While existing research has highlighted the adaptive migratory capabilities of locusts, the evolutionary patterns of their migration remain elusive...

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Transcriptomic analysis of Virescentia guangxiensis (Rhodophyta: Batrachospermales) revealed differential expression of genes in gametophyte and chantransia life phases

The genus Virescentia is a significant member of the Batrachospermaceae, exhibiting distinctive life history characteristics defined by alternating generations. This group of taxa has specific environmental requi...

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Identification and analysis of the GATA gene family in onion (Allium cepa L.) in response to chromium and salt stress

The GATA transcription factors play multifaceted roles in modulating vital physiological processes in plants. However, the GATA transcription factor family in onion (Allium cepa L.) has been explored to a limited...

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Integrative transcriptomic and metabolomic analyses reveal the role of melatonin in promoting secondary hair follicle development in cashmere goats

Melatonin improves the production performance of animal furs, particularly in promoting wool and cashmere growth. Although most studies of melatonin enhancing cashmere growth have focused primarily on gene and...

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Mitogenome of Uncaria rhynchophylla: genome structure, characterization, and phylogenetic relationships

Uncaria rhynchophylla is listed in the Chinese pharmacopoeia as one of the five botanical sources of the traditional medicine Gou-Teng, which has been utilized for the treatment of mental and cardiovascular disor...

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A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency

Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits t...

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Data-driven projections of candidate enhancer-activating SNPs in immune regulation

Millions of single nucleotide polymorphisms (SNPs) have been identified in humans, but the functionality of almost all SNPs remains unclear. While current research focuses primarily on SNPs altering one amino ...

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Physiological and transcriptomic evidence revealed the role of exogenous GABA in enhancing salt tolerance in strawberry seedlings

As one of the most salt-sensitive crops, strawberry production is severely limited by salt stress. γ--aminobutyric acid (GABA) has been reported to play an important role in the immune response of plants. In t...

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Transcriptomics insights into glutamine on repairing of histamine-induced Yak rumen epithelial cells barrier damage in vitro

Glutamine (Gln) plays a pivotal role in maintaining the integrity of the rumen epithelial barrier in mammals. This study aimed to investigate the effects of Gln on histamine-induced barrier damage in yak rumen...

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An algorithm for annotation and classification of T. cruzi MASP sequences: towards a better understanding of the parasite genetic variability

Trypanosoma cruzi, the protozoan causing Chagas disease, is responsible for a neglected tropical disease affecting millions in Latin America. Its genome contains rapidly evolving multigene families, such as mucin...

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MARSweb: a fully automated web service for set-based association testing

Despite the successes in GWAS, there is still a large gap between the known heritability and the part explained by the SNPs identified by GWAS. Set-based analysis is one of the approaches that has tried to ide...

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Genetic and metabolic insights into sexual dimorphism in the flexor carpi radialis of Asiatic toads (Bufo gargarizans) associated with amplexus behavior

Sexual dimorphism, a widespread phenomenon across the animal kingdom, encompasses differences between sexes in size, morphology, and physiological traits. In this study, we investigated sexual dimorphism in th...

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Identification through a transcriptomic approach of candidate genes involved in the adaptation of the cyst nematode Globodera pallida to the potato resistance factor GpaV_vrn

Since the banning of chemical products used to control plant-parasitic nematode populations, the use of resistant plants has become the most effective management approach against the potato cyst nematode Globoder...

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Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli

The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolut...

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Eggs-posed: revision of Schistosoma mansoni venom allergen-like proteins unveils new genes and offers new insights into egg-host interactions

Venom allergen-like proteins (VALs) are abundant in the excretory-secretory products (ESPs) of numerous parasitic helminths and have been extensively studied for over 30 years because of their potential to int...

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M6A methyltransferase METTL3 promotes glucose metabolism hub gene expression and induces metabolic dysfunction-associated steatotic liver disease (MASLD)

N6-methyladenosine (m6A) RNA modification plays a crucial role in various biological events and is implicated in various metabolic-related diseases. However, its role in MASLD remains unclear. This study aims ...

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Single-cell RNA transcriptome uncovers distinct developmental trajectories in the embryonic skeletal muscle of Daheng broiler and Tibetan chicken

Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is ...

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Mechanisms underlining Kelp (Saccharina japonica) adaptation to relative high seawater temperature

Saccharina japonica has been cultivated in China for almost a century. From Dalian to Fujian, the lowest and the highest seawater temperatures in the period of cultivation increased by 14℃ and 8℃, respectively. I...

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Assembly and analysis of stephania japonica mitochondrial genome provides new insights into its identification and energy metabolism

Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for i...

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Development of single nucleotide polymorphisms in key genes of taurine and betaine metabolism in Crassostrea hongkongensis and their association with content-related traits

Taurine and betaine are important nutrients in the Hong Kong oyster (Crassostrea hongkongensis) and have many important biological properties. To investigate the characteristics of taurine and betaine and identif...

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Time-course RNA-seq analysis of upland cotton (Gossypium hirsutum L.) responses to Southern root-knot nematode (Meloidogyne incognita) during compatible and incompatible interactions

The Southern root-knot nematode (Meloidogyne incognita) poses a substantial threat to cotton (Gossypium hirsutum L.) by causing significant agricultural losses. Host plant resistance is the most plausible approac...

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Anthocyanin metabolites and related regulatory genes analysis in leaves of Acer Pseudosieboldianum mutant during different periods of color change

Acer pseudosieboldianum (Pax) Komarov, is a colorful leaf species belonging to the family Aceraceae, mainly distributed in Northeast China, Russia, and northern Korea. The leaves of Acer pseudosieboldianum are gr...

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Pan-WD40ome analysis of 26 diverse inbred lines reveals the structural and functional diversity of WD40 proteins in maize

The WD40 repeat proteins are crucial components of eukaryotic genomes and contribute to a wide array of plant developmental processes and environmental interactions. However, the true extent of intraspecific W...

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Genome-wide identification and analysis of the UBA2 gene family in wheat (Triticum aestivum L.)

RNA-binding proteins (RBPs) participate in multiple aspects of RNA metabolism, which in turn regulates gene expression, thereby involving in organism growth and development. The UBA2 family, one of the subfami...

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Physiological and transcriptomic analyses revealed the alleviating effects of exogenous Ca²⁺ and NO compound treatment on high salt stress in Reaumuria soongorica

Soil salinization represents the most prevalent abiotic stress, severely impacting a severe impact on plant growth and crop yield. Consequently, delving into the mechanism through which exogenous substances en...

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Integrating QTL mapping with transcriptome analysis mined candidate genes of growth stages in castor (Ricinus communis L.)

The growth stages largely determine the crop yield, while little is known about their genetic mechanisms in castor. In this study, the QTL mapping and candidate gene mining of growth stages were conducted usin...

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Transcriptome analysis of interna rootlets of the rhizocephalan Parasacculina sinensis reveals potential mechanisms of parasite host control

The endoparasitic rhizocephalan Parasacculina sinensis has a radically simplified morphology and primarily infests decapods crustaceans. Rhizocephalan barnacles usually absorb nutrients from the host through a co...

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Transcriptome reveal gene regulation mechanisms of the barnacle Chthamalus challengeri for microhabitat adaption in the intertidal zone

Microhabitat environmental factors (e.g., temperature, oxygen concentration, nutrients, osmotic stress, and topography) are critical to the survival of intertidal organisms. Understanding how transcription res...

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The intensity of the transcriptional response varies across infection with distinct viral strains in an insect host

Organisms respond to infectious agents through diverse immune strategies, and may need to cater a specific response to distinct pathogen challenges, such as various strains of a virus, to maximize fitness. Def...

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Validation of loci and genes associated with fertility in Holstein cows using gene-set enrichment analysis-SNP and genotype-by-sequencing

The financial strain fertility issues cause the dairy cattle industry is substantial, with over $7 billion in lost revenue accrued annually due to a relatively low cow conception rate (CCR; 30–43%) for US dair...

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Genome-wide identification of the AAAP gene family and expression analysis under tissue-specific expression in five legumes

Amino acid/auxin permease (AAAP) is a transcription factor with a highly conserved amino acid region that regulates physiological processes and development in many plants and responds to various abiotic stresses....

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Correction: Identification of crucial LncRNAs associated with testicular development and LOC108635509 as a potential regulator in black goat spermatogenesis

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Improving genomic prediction of vitamin C content in spinach using GWAS-derived markers

Vitamin C (VC), also known as ascorbic acid and ascorbate, is a water-soluble antioxidant in plants that promotes skin health and immune function in humans. Spinach (Spinacia oleracea L.) is a leafy green widely ...

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Interaction of genetic variants and methylation in transcript-level expression regulation in Alzheimer’s disease by multi-omics data analysis

Alzheimer’s disease (AD) presents a significant public health problem and major cause of dementia. Not only genetic but epigenetic factors contribute to complex and heterogeneous molecular mechanisms underlyin...

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Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics

Common bean (Phaseolus vulgaris), a staple food in Latin America and Africa, serves as a vital source of energy, protein, and essential minerals for millions of people. However, genomics knowledge that breeders c...

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Genome-wide identification, characterization and expression analysis of the chalcone synthase gene family in Chinese cabbage

Chalcone synthase (CHS) is a key rate-limiting enzyme in the flavonoid synthesis pathway. Flavonoids are crucial secondary metabolites that play significant roles in plant growth, development, and stress resis...

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Histone H3 K4 trimethylation occurs mainly at the origins of polycistronic transcription in the genome of Leishmania infantum promastigotes and intracellular amastigotes

Trypanosomatids include the genera Trypanosoma and Leishmania, which are the etiological agents of important human diseases. These pathogens present unique mechanisms of gene expression characterized by functiona...

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