Articles

Mitogenomic phylogeny and divergence time estimation of Artemia Leach, 1819 (Branchiopoda: Anostraca) with emphasis on parthenogenetic lineages

The brine shrimp Artemia, a crustacean adapted to the extreme conditions of hypersaline environments, comprises nine regionally distributed sexual species scattered (island-like) over heterogeneous environments a...

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LungGENIE: the lung gene-expression and network imputation engine

Few cohorts have study populations large enough to conduct molecular analysis of ex vivo lung tissue for genomic analyses. Transcriptome imputation is a non-invasive alternative with many potential applications. ...

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Phylogenetic analysis of Asiatic species in the tropical genus Beilschmiedia (Lauraceae)

The tropial genus Beilschmiedia, comprising over 250 species worldwide, includes approximately 40 species distributed in the northern tropical forests of Asia. However, the phylogenetic relationships among these ...

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Post-transcriptional regulation in early cell fate commitment of germ layers

Cell differentiation during development is orchestrated by precisely coordinated gene expression programs. While some regulatory mechanisms are well understood, there is a significant room to explore unresolve...

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High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot on chromosome A01

Peanut (Arachis hypogaea L.) is a vital global crop, frequently threatened by both abiotic and biotic stresses. Among the most damaging biotic stresses is Tomato spotted wilt virus (TSWV), which causes peanut spo...

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The roles of a MiRNA and its targeted methyltransferase 3 in carotenoid accumulation in adductor muscles of QN orange scallops

QN Orange scallops are interspecific hybrids with orange adductor muscles that are rich in carotenoids. In this study, analysis of miRNA expression profiles was performed to explore possible regulatory pattern...

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The case-only design is a powerful approach to detect interactions but should be used with caution

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A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development

Cotton fiber development relies on complex and intricate biological processes to transform newly differentiated fiber initials into the mature, extravagantly elongated cellulosic cells that are the foundation ...

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Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the “Valley of the Kings”, Tuva

In the I^st millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style ...

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DSLE2 random-effects meta-analysis model for high-throughput methylation data

With the rapid development of high-throughput sequencing technology, high-throughput sequencing data has grown on a massive scale, leading to the emergence of multiple public databases, such as EBI and GEO. Co...

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Analysis and identification of mitochondria-related genes associated with age-related hearing loss

To explore the mitochondrial genes that play a key role in the occurrence and development of age-related hearing loss (ARHL) and provide a basis for the study of the mechanism of ARHL.

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Cas9-expressing cattle using the PiggyBac transposon all-in-one system

Livestock, particularly cattle, are crucial for biotechnology fields, such as genetic breeding, infectious diseases, bioreactors, and specific disease models. However, genetic engineering in cattle has lagged ...

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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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Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance

Integrating germplasm populations genotyped by different genotyping platforms via genotype imputation is a way to utilize accumulated genetic resources. In this study, we used 278 canola samples genotyped via ...

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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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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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