journal
https://read.qxmd.com/read/38418975/the-structure-and-diversity-of-bacteria-and-fungi-in-the-roots-and-rhizosphere-soil-of-three-different-species-of-geodorum
#1
JOURNAL ARTICLE
Jianxiu Liu, Danjuan Zeng, Yang Huang, Lisha Zhong, Jialin Liao, Yuxing Shi, Haidu Jiang, Yajin Luo, Yu Liang, Shengfeng Chai
Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA...
February 28, 2024: BMC Genomics
https://read.qxmd.com/read/38418960/differential-regulation-of-mirnas-involved-in-the-susceptible-and-resistance-responses-of-wheat-cultivars-to-wheat-streak-mosaic-virus-and-triticum-mosaic-virus
#2
JOURNAL ARTICLE
Inanc Soylu, Dilip K Lakshman, Satyanarayana Tatineni, Leny C Galvez, Amitava Mitra
BACKGROUND: Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are components of the wheat streak mosaic virus disease complex in the Great Plains region of the U.S.A. and elsewhere. Co-infection of wheat with WSMV and TriMV causes synergistic interaction with more severe disease symptoms compared to single infections. Plants are equipped with multiple antiviral mechanisms, of which regulation of microRNAs (miRNAs) is a potentially effective constituent. In this investigation, we have analyzed the total and relative expression of miRNA transcriptome in two wheat cultivars, Arapahoe (susceptible) and Mace (temperature-sensitive-resistant), that were mock-inoculated or inoculated with WSMV, TriMV, or both at 18 °C and 27 °C...
February 28, 2024: BMC Genomics
https://read.qxmd.com/read/38413941/mitochondrial-genome-structure-and-composition-in-70-fishes-a-key-resource-for-fisheries-management-in-the-south-atlantic
#3
JOURNAL ARTICLE
Marcela Alvarenga, Ananda Krishna Pereira D'Elia, Graciane Rocha, Clara Alvarez Arantes, Frederico Henning, Ana Tereza Ribeiro de Vasconcelos, Antonio Mateo Solé-Cava
BACKGROUND: Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413914/a-preliminary-study-of-the-mirna-restitution-effect-on-cnv-induced-mirna-downregulation-in-cakut
#4
JOURNAL ARTICLE
Kristina Mitrovic, Ivan Zivotic, Ivana Kolic, Jelena Zakula, Maja Zivkovic, Aleksandra Stankovic, Ivan Jovanovic
BACKGROUND: The majority of CAKUT-associated CNVs overlap at least one miRNA gene, thus affecting the cellular levels of the corresponding miRNA. We aimed to investigate the potency of restitution of CNV-affected miRNA levels to remediate the dysregulated expression of target genes involved in kidney physiology and development in vitro. METHODS: Heterozygous MIR484 knockout HEK293 and homozygous MIR185 knockout HEK293 cell lines were used as models depicting the deletion of the frequently affected miRNA genes by CAKUT-associated CNVs...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413907/combined-analysis-of-mrna-and-mirna-transcriptomes-reveals-the-regulatory-mechanism-of-xanthomonas-arboricola-pv-pruni-resistance-in-prunus-persica
#5
JOURNAL ARTICLE
Pengxiang Zhu, Haiyan Li, Tailiang Lu, Ruizheng Liang, Baoxiong Wan
BACKGROUND: Peach bacterial shot hole, caused by Xanthomonas arboricola pv pruni (Xap), is a global bacterial disease that poses a threat to the yield and quality of cultivated peach trees (Prunus persica). RESULTS: This study compared the mRNA and miRNA profiles of two peach varieties, 'Yanbao' (resistant) and 'Yingzui' (susceptible), after inoculation with Xap to identify miRNAs and target genes associated with peach tree resistance. mRNA sequencing results revealed that in the S0-vs-S3 comparison group, 1574 genes were upregulated and 3975 genes were downregulated...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413905/subtelomeric-plasticity-contributes-to-gene-family-expansion-in-the-human-parasitic-flatworm-schistosoma-mansoni
#6
JOURNAL ARTICLE
T Brann, A Beltramini, C Chaparro, M Berriman, S R Doyle, A V Protasio
BACKGROUND: The genomic region that lies between the telomere and chromosome body, termed the subtelomere, is heterochromatic, repeat-rich, and frequently undergoes rearrangement. Within this region, large-scale structural changes enable gene diversification, and, as such, large multicopy gene families are often found at the subtelomere. In some parasites, genes associated with proliferation, invasion, and survival are often found in these regions, where they benefit from the subtelomere's highly plastic, rapidly changing nature...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413895/transcriptomics-and-metabolomics-analysis-reveal-the-dietary-copper-deficiency-and-supplementation-effects-of-liver-gene-expression-and-metabolite-change-in-grazing-sheep
#7
JOURNAL ARTICLE
Xiwei Jin, Lingbo Meng, Zhi Qi, Lan Mi
BACKGROUND: The appropriate mineral nutrients are essential for sheep growth and reproduction. However, traditional grazing sheep often experience mineral nutrient deficiencies, especially copper (Cu), due to inadequate mineral nutrients from natural pastures. RESULTS: The results indicated that dietary Cu deficiency and supplementation significantly reduced and elevated liver concentration of Cu, respectively (p < 0.05). FOXO3, PLIN1, ACTN2, and GHRHR were identified as critical genes using the weighted gene co-expression network analysis (WGCNA), quantitative real-time polymerase chain reaction (qRT-PCR), and receiver operating characteristic curve (ROC) validation as potential biomarkers for evaluating Cu status in grazing sheep...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413888/rna-sequencing-identifies-key-genes-involved-in-intramuscular-fat-deposition-in-chickens-at-different-developmental-stages
#8
JOURNAL ARTICLE
Jinmei Zhu, Yongli Wang, Yongchun Su, Maiqing Zheng, Huanxian Cui, Zhiwu Chen
BACKGROUND: Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality. RESULTS: In this study, we used 30 RNA sequences generated from the transcriptome of chicken breast muscle tissues at different developmental stages to construct a gene expression matrix to map RNA sequence reads to the chicken genome and identify the transcript of origin...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413855/pangenome-analysis-of-shewanella-xiamenensis-revealed-important-genetic-traits-concerning-genetic-diversity-pathogenicity-and-antibiotic-resistance
#9
JOURNAL ARTICLE
Haichen Wang, Fengjun Xia, Yubing Xia, Jun Li, Yongmei Hu, Yating Deng, Mingxiang Zou
BACKGROUND: Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis. RESULTS: Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38413848/identification-of-common-stria-vascularis-cellular-alteration-in-sensorineural-hearing-loss-based-on-scrna-seq
#10
JOURNAL ARTICLE
Xi Gu, Kanglun Jiang, Ruru Chen, Zhifeng Chen, Xianmin Wu, Haijie Xiang, Xinsheng Huang, Benyu Nan
BACKGROUND: The stria vascularis (SV), located in the lateral wall of the cochlea, maintains cochlear fluid homeostasis and mechanoelectrical transduction (MET) activity required for sound wave conduction. The pathogenesis of a number of human inheritable deafness syndromes, age related hearing loss, drug-induced ototoxicity and noise-induced hearing loss results from the morphological changes and functional impairments in the development of the SV. In this study, we investigate the implications of intercellular communication within the SV in the pathogenesis of sensorineural hearing loss (SNHL)...
February 27, 2024: BMC Genomics
https://read.qxmd.com/read/38408933/body-mass-index-stratified-meta-analysis-of-genome-wide-association-studies-of-polycystic-ovary-syndrome-in-women-of-european-ancestry
#11
JOURNAL ARTICLE
Kharis Burns, Benjamin H Mullin, Loes M E Moolhuijsen, Triin Laisk, Jaakko S Tyrmi, Jinrui Cui, Ky'Era V Actkins, Yvonne V Louwers, Lea K Davis, Frank Dudbridge, Ricardo Azziz, Mark O Goodarzi, Hannele Laivuori, Reedik Mägi, Jenny A Visser, Joop S E Laven, Scott G Wilson, Felix R Day, Bronwyn G A Stuckey
BACKGROUND: Polycystic ovary syndrome (PCOS) is a complex multifactorial disorder with a substantial genetic component. However, the clinical manifestations of PCOS are heterogeneous with notable differences between lean and obese women, implying a different pathophysiology manifesting in differential body mass index (BMI). We performed a meta-analysis of genome-wide association study (GWAS) data from six well-characterised cohorts, using a case-control study design stratified by BMI, aiming to identify genetic variants associated with lean and overweight/obese PCOS subtypes...
February 26, 2024: BMC Genomics
https://read.qxmd.com/read/38408914/dietary-antarctic-krill-improves-antioxidant-capacity-immunity-and-reduces-lipid-accumulation-insights-from-physiological-and-transcriptomic-analysis-of-plectropomus-leopardus
#12
JOURNAL ARTICLE
Mengya Wang, Shaoxuan Wu, Hui Ding, Mingyi Wang, Jiayi Ma, Jie Xiao, Bo Wang, Zhenmin Bao, Jingjie Hu
BACKGROUND: Due to its enormous biomass, Antarctic krill (Euphausia superba) plays a crucial role in the Antarctic Ocean ecosystem. In recent years, Antarctic krill has found extensive application in aquaculture, emerging as a sustainable source of aquafeed with ideal nutritional profiles. However, a comprehensive study focused on the detailed effects of dietary Antarctic krill on aquaculture animals, especially farmed marine fishes, is yet to be demonstrated. RESULTS: In this study, a comparative experiment was performed using juvenile P...
February 26, 2024: BMC Genomics
https://read.qxmd.com/read/38408895/transcriptomic-divergence-of-the-rheum-palmatum-complex-derived-from-top-geoherb-and-non-geoherb-areas-provides-the-insights-into-geoherbalism-properties-of-rhubarb
#13
JOURNAL ARTICLE
Tao Zhou, Yadi Tang, Lipan Zhou, Jie Liu, Yang Pu, Fan Jiang, Jian Wang, Xumei Wang
Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. However, few researches were conducted to clarify the geoherbalism based on a large scale of transcriptomics. In the present study, we compared the transcriptomes of Rheum palmatum complex derived from top-geoherb and non-geoherb areas to show the geoherbalism properties of rhubarb. A total of 412.32 Gb clean reads were obtained with unigene numbers of 100,615 after assembly...
February 26, 2024: BMC Genomics
https://read.qxmd.com/read/38408894/characterization-of-sucrose-nonfermenting-1-related-protein-kinase-2-snrk2-gene-family-in-haynaldia-villosa-demonstrated-snrk2-9-v-enhances-drought-and-salt-stress-tolerance-of-common-wheat
#14
JOURNAL ARTICLE
Jia Liu, Luyang Wei, Yirong Wu, Zongkuan Wang, Haiyan Wang, Jin Xiao, Xiue Wang, Li Sun
BACKGROUND: The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. RESULTS: To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions...
February 26, 2024: BMC Genomics
https://read.qxmd.com/read/38408892/correction-genome-wide-association-study-for-stayability-at-diferent-calvings-in-nellore-beef-cattle
#15
Diogo Osmar Silva, Gerardo Alves Fernandes Júnior, Larissa Fernanda Simielli Fonseca, Lúcio Flávio Macedo Mota, Tiago Bresolin, Roberto Carvalheiro, Lucia Galvão de Albuquerque
No abstract text is available yet for this article.
February 26, 2024: BMC Genomics
https://read.qxmd.com/read/38395786/an-immunogenic-cell-death-related-gene-expression-signature-in-predicting-prognosis-of-pancreatic-ductal-adenocarcinoma
#16
JOURNAL ARTICLE
Xiaobo Wang, Tianxiang Ren, Chuting Liao, Yong Xie, Jing Cao
BACKGROUND: Immunogenic cell death (ICD) has been identified as regulated cell death, which is sufficient to activate the adaptive immune response. This study aimed to research ICD-related genes and create a gene model to predict pancreatic ductal adenocarcinoma (PAAD) patients' prognosis. METHODS: The RNA sequencing and clinical data were downloaded from the TGCA and GEO databases. The PAAD samples were classified into two subtypes based on the expression levels of ICD-related genes using consensus clustering...
February 23, 2024: BMC Genomics
https://read.qxmd.com/read/38395768/genome-assembly-of-medicago-truncatula-accession-sa27063-provides-insight-into-spring-black-stem-and-leaf-spot-disease-resistance
#17
JOURNAL ARTICLE
Jacob R Botkin, Andrew D Farmer, Nevin D Young, Shaun J Curtin
Medicago truncatula, model legume and alfalfa relative, has served as an essential resource for advancing our understanding of legume physiology, functional genetics, and crop improvement traits. Necrotrophic fungus, Ascochyta medicaginicola, the causal agent of spring black stem (SBS) and leaf spot is a devasting foliar disease of alfalfa affecting stand survival, yield, and forage quality. Host resistance to SBS disease is poorly understood, and control methods rely on cultural practices. Resistance has been observed in M...
February 23, 2024: BMC Genomics
https://read.qxmd.com/read/38395755/alteration-of-chromosome-structure-impacts-gene-expressions-implicated-in-pancreatic-ductal-adenocarcinoma-cells
#18
JOURNAL ARTICLE
Wenrui Han, Detong Shi, Qiu Yang, Xinxin Li, Jian Zhang, Cheng Peng, Fang Yan
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a five-year survival rate of approximately 10%. Genetic mutations are pivotal drivers in PDAC pathogenesis, but recent investigations also revealed the involvement of non-genetic alterations in the disease development. In this study, we undertook a multi-omics approach, encompassing ATAC-seq, RNA-seq, ChIP-seq, and Hi-C methodologies, to dissect gene expression alterations arising from changes in chromosome accessibility and chromatin three-dimensional interactions in PDAC...
February 23, 2024: BMC Genomics
https://read.qxmd.com/read/38395740/integrated-metabolomics-and-transcriptomics-analysis-highlight-key-pathways-involved-in-the-somatic-embryogenesis-of-darjeeling-tea
#19
JOURNAL ARTICLE
Vivek Kumar Awon, Debabrata Dutta, Saptadipa Banerjee, Soumili Pal, Gaurab Gangopadhyay
BACKGROUND: Darjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor seed germination, and viability, as well as issues with vegetative propagation. Somatic embryogenesis (SE) is a valuable method for rapid clonal propagation of Darjeeling tea. However, the metabolic regulatory mechanisms underlying SE in Darjeeling tea remain largely unknown. To address this, we conducted an integrated metabolomics and transcriptomics analysis of embryogenic callus (EC), globular embryo (GE), and heart-shaped embryo (HE)...
February 23, 2024: BMC Genomics
https://read.qxmd.com/read/38389079/characterization-of-firmiana-danxiaensis-plastomes-and-comparative-analysis-of-firmiana-insight-into-its-phylogeny-and-evolution
#20
JOURNAL ARTICLE
Ya-Li Li, Li-Yun Nie, Shuang-Wen Deng, Lei Duan, Zheng-Feng Wang, Joseph L M Charboneau, Boon-Chuan Ho, Hong-Feng Chen
BACKGROUND: Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies...
February 22, 2024: BMC Genomics
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