Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) DOI Creative Commons
Lei Zhang, Wanting Zhang,

Yingyin Cheng

et al.

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: Jan. 26, 2025

Abstracts The large-scale loach ( Paramisgurnus dabryanus ; Cypriniformes: Cobitidae) is primarily distributed in East Asia. It an important economic fish species characterized by fast growth, temperature-dependent sex determination and the ability to breathe air. Currently, molecular mechanism studies related some aspects such as determination, toxicology, feed nutrition, growth genetic evolution have been conducted. However, lack of a high-quality reference genome has hindered further research. In this study, we performed PacBio HiFi Hi-C sequencing on female (ZW) specimen assembled first chromosome-level loach. comprises 24 chromosomes, with total length 1.04 Gb, scaffold N50 41.7 Mb, BUSCO completeness 95.8%, including 28,311 protein-coding genes. These findings not only provide new insights into structure but also establish crucial point for omics serve essential genomic resource breeding programs species.

Language: Английский

TCMPG: an integrative database for traditional Chinese medicine plant genomes DOI Creative Commons
Fanbo Meng, Qiang Tang,

Tianzhe Chu

et al.

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Abstract Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development high-throughput sequencing technology, genomes many been sequenced. Storing analyzing volume genomic data has become an urgent task. To solve this challenge, we proposed Traditional Chinese Medicine Plant Genome database (TCMPG, http://cbcb.cdutcm.edu.cn/TCMPG/), integrative for storing scattered plants. TCMPG currently includes 160 plants, 195 corresponding genomes, 255 herbal medicines. Detailed information on plant species, medicines is also integrated into TCMPG. Popular analysis tools are embedded in to facilitate systematic These include BLAST identifying orthologs from different SSR Finder simple sequence repeats, JBrowse browsing Synteny Viewer displaying syntenic blocks between two HmmSearch protein domains. will be continuously updated by integrating new comparative functional analysis.

Language: Английский

Citations

29
GhWRKY55 as a negative regulator of cotton resistance to Verticillium dahliae via lignin biosynthetic and jasmonic acid signaling pathways DOI

Xueyuan Ma,

Bin Chen, Yang Li

et al.

Industrial Crops and Products, Journal Year: 2024, Volume and Issue: 210, P. 118154 - 118154

Published: Jan. 31, 2024

Language: Английский

Citations

6
Ancient genomes revealed the complex human interactions of the ancient western Tibetans DOI Creative Commons
Fan Bai, Yichen Liu,

Shargan Wangdue

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(12), P. 2594 - 2605.e7

Published: May 22, 2024

The western Tibetan Plateau is the crossroad between Plateau, Central Asia, and South it a potential human migration pathway connecting these regions. However, population history of remains largely unexplored due to lack ancient genomes covering long-time interval from this area. Here, we reported genome-wide data 65 individuals dated 3,500-300 years before present (BP) in Ngari prefecture. populations share majority their genetic components with southern have maintained continuity since 3,500 BP while maintaining interactions within outside Plateau. Within were influenced by additional expansion south southwest plateau 1,800 BP. Outside interacted both Asian at least 2,000 ago, Asian-related influence, despite being very limited, was Indus Valley Civilization (IVC) migrants Asia instead IVC Valley. In light new data, our study revealed complex interconnections across

Language: Английский

Citations

6
Comparative genomic sequencing to characterize Mycoplasma pneumoniae genome, typing, and drug resistance DOI Creative Commons
Yue Jiang, Hailong Kang, Haiwei Dou

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(8)

Published: June 21, 2024

ABSTRACT To analyze the characteristics of Mycoplasma pneumoniae as well macrolide antibiotic resistance through whole-genome sequencing and comparative genomics. Thirteen clinical strains isolated from 2003 to 2019 were selected, 10 which resistant erythromycin (MIC >64 µg/mL), including 8 P1-type I 2 II. Three sensitive (<1 µg/mL) One strain had an A→G point mutation at position 2064 in region V 23S rRNA, others it 2063, while three no here. Genome assembly genome analysis revealed a high level consistency within P1 type, primary differences sequences concentrated encoding protein. In II strains, specific gene mutations identified: C162A A430G L4 T1112G CARDS gene. Clinical information showed seven cases diagnosed with severe pneumonia, all infected drug-resistant strains. Notably, BS610A4 CYM219A1 exhibited multi-copy phenomenon shared conserved functional domain DUF31 protein family. Clinically, patients refractory pleural effusion, necessitating treatment glucocorticoids bronchoalveolar lavage. The variations between occur among different P1-types, there is genomic P1-types. loci associated types identified, genetic alterations directly related presentation observed. IMPORTANCE important pathogen community-acquired brings difficulties treatment. We analyzed M. work addressed that All pneumonia drug-resistant, two phenomenon, sharing

Language: Английский

Citations

6
Single-cell and Spatial Transcriptomics Reveals Ferroptosis as The Most Enriched Programmed Cell Death Process in Hemorrhage Stroke-induced Oligodendrocyte-mediated White Matter Injury DOI Creative Commons

Lingui Gu,

Hualin Chen,

Ruxu Geng

et al.

International Journal of Biological Sciences, Journal Year: 2024, Volume and Issue: 20(10), P. 3842 - 3862

Published: Jan. 1, 2024

Intracerebral hemorrhage (ICH) is a severe stroke subtype with limited therapeutic options.Programmed cell death (PCD) crucial for immunological balance, and includes necroptosis, pyroptosis, apoptosis, ferroptosis, necrosis.However, the distinctions between these programmed modalities after ICH remain to be further investigated.We used single-cell transcriptome (single-cell RNA sequencing) spatial (spatial techniques investigate PCD-related gene expression trends in rat brain following hemorrhagic stroke.Ferroptosis was main PCD process ICH, primarily affected mature oligodendrocytes.Its onset occurred as early 1 hour post-ICH, peaking at 24 hours post-ICH.Additionally, ferroptosis-related genes were distributed hippocampus choroid plexus.We also elucidated specific interaction lipocalin-2 (LCN2)-positive microglia oligodendrocytes that mediated by colony stimulating factor (CSF1)/CSF1 receptor pathway, leading ferroptosis induction subsequent neurological deficits.In conclusion, our study highlights primary mechanism, emerging post-ICH.Early intervention via suppression of microglial LCN2 may alleviate ferroptosis-induced damage associated deficits, thus offering promising neuroprotective strategy ICH.

Language: Английский

Citations

6
Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations DOI Creative Commons

Qian Su,

Daohua Zhuang,

Yuchun Li

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 28, 2024

The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in under such conditions existence of any dominant or core bacteria that may assist host acclimatization.

Language: Английский

Citations

6
Integrative multiomics analysis identifies molecular subtypes and potential targets of hepatocellular carcinoma DOI Creative Commons
Shuai Yang, Lu Zheng, Lingling Li

et al.

Clinical and Translational Medicine, Journal Year: 2024, Volume and Issue: 14(6)

Published: May 28, 2024

Abstract Background The liver is anatomically divided into eight segments based on the distribution of Glisson's triad. However, molecular mechanisms underlying each segment and its association with hepatocellular carcinoma (HCC) heterogeneity are not well understood. In this study, our objective to conduct a comprehensive multiomics profiling segmentation atlas in order investigate potential subtypes therapeutic approaches for HCC. Methods A high throughput liquid chromatography‐tandem mass spectrometer strategy was employed comprehensively analyse proteome, lipidome metabolome data, focus segment‐resolved profiling. To classify HCC subtypes, obtained data normal reference were integrated. Additionally, targets identified using immunohistochemistry assays. effectiveness these further validated through patient‐derived organoid (PDO) Results 8536 high‐confidence proteins, 1029 polar metabolites 3381 nonredundant lipids performed analysis revealed that adjacent tissues, left lobe primarily involved energy metabolism, while right associated small molecule metabolism. Based atlas, patients classification three subtypes. C1 subtype showed enrichment ribosome biogenesis, C2 exhibited an intermediate phenotype, C3 closely neutrophil degranulation. Furthermore, PDO assay, exportin 1 (XPO1) 5‐lipoxygenase (ALOX5) as respectively. Conclusion Our extensive defines uncovers strategies have enhance prognosis

Language: Английский

Citations

5
Germline variants in UNC13D and AP3B1 are enriched in COVID-19 patients experiencing severe cytokine storms DOI Creative Commons
Hui Luo, Dan Liu, Wenbing Liu

et al.

European Journal of Human Genetics, Journal Year: 2021, Volume and Issue: 29(8), P. 1312 - 1315

Published: April 19, 2021

Abstract Critically ill coronavirus disease 2019 (COVID-19) is characterized by severe cytokine storms, a hyperinflammatory condition intimately related to the development of fatal outcomes. Why some individuals seem particularly vulnerable storms still unknown. Primary immunodeficiency (PID)-related genes are inherited factors that dysregulate host inflammatory responses infection, especially hemophagocytic lymphohistiocytosis (HLH)-related genes, established as contributors excessive storms. We analyzed association between PID gene variants with in COVID-19. conducted whole-exome sequencing 233 hospitalized COVID-19 patients and identified four ( UNC13D , AP3B1 RNF168 DHX58 ) were significantly enriched experiencing The total percentage or two typical HLH was dramatically higher high-level group than low-level (33.3 vs. 5.7%, P < 0.001). Germline associated outcomes These findings advance understanding individual susceptibility help optimize current management

Language: Английский

Citations

31
GenBase: A Nucleotide Sequence Database DOI Creative Commons
Cuiping BU, Xinchang Zheng, Xuetong Zhao

et al.

Genomics Proteomics & Bioinformatics, Journal Year: 2024, Volume and Issue: 22(3)

Published: June 1, 2024

The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth sequence data efficiently on time. To address this issue, we present GenBase (https://ngdc.cncb.ac.cn/genbase), an open-access repository that follows International Nucleotide Sequence Database Collaboration (INSDC) standards structures, for efficient nucleotide archiving, searching, sharing. As a core resource within National Genomics Data Center (NGDC) China Bioinformation (CNCB; https://ngdc.cncb.ac.cn), offers bilingual submission pipeline services, as well local assistance China. also provides unique Excel format metadata description feature annotation sequences, along with real-time validation system to streamline submissions. April 23, 2024, received 68,251 sequences 689,574 annotated protein across 414 species from 2319 Out these, 63,614 (93%) 620,640 (90%) have been released are publicly accessible through GenBase's web search system, File Transfer Protocol (FTP), Application Programming Interface (API). Additionally, collaboration INSDC, has constructed effective exchange mechanism GenBank started sharing sequences. Furthermore, integrates all daily updates, demonstrating its commitment actively contributing global management

Language: Английский

Citations

4
Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer DOI Creative Commons
Yue Xue, Lu Liu, Ye Zhang

et al.

Molecular Cancer, Journal Year: 2024, Volume and Issue: 23(1)

Published: Sept. 6, 2024

Language: Английский

Citations

4