Zhu, Z., Zheng, L., Pan, L., Hsiang, T., and Huang, J. 2014. Identification and characterization of Fusarium species associated with wilt of Eleocharis dulcis (Chinese water chestnut) in China. Plant Dis. 98:977-987.Fusarium wilt is one of the most important diseases of Eleocharis dulcis (Chinese water chestnut) in China. In order to characterize the pathogens responsible, 69 Fusarium isolates were collected from diseased plants in E. dulcis production areas of the Chinese provinces Anhui, Fujian, Hubei, Hunan, Jiangsu, and Zhejiang. These were then identified based on morphological and molecular characteristics. F. commune was the most common species (92.8%) and was widely distributed in the six provinces. A novel species within the Gibberella fujikuroi species complex (GFSC) was found in Hubei and Zhejiang provinces (5.8%), and an unidentified Fusarium sp. was found only in Hubei province (1.4%). Thirty F. commune isolates from different provinces and four GFSC isolates were selected for sequence analyses of the translation elongation factor 1-α (EF-1α), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the nuclear ribosomal intergenic spacer region (IGS). Maximum parsimony and Bayesian analyses of the multilocus sequence data of these two species plus other taxa showed that the two species formed two distinct, well-supported clades among the three individual and combined gene genealogies. Isolates from different locations were scattered, with no evidence of geographic specialization. Pathogenicity assays showed that the two Fusarium spp., including the unidentified Fusarium sp., were pathogenic to E. dulcis 'Tuanfeng seven'. There was no relationship between the source of isolates and their pathogenicity. This is the first description of F. commune, a novel species within the GFSC, and an unidentified Fusarium sp. as causal agents of Fusarium wilt of E. dulcis in China.
DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb, www.dna-asmdb.com).
Ethylene promotes ripening in fruits as well as the biosynthesis of anthocyanins in plants. However, the question of which ethylene response factors (ERFs) interact with the genes along the anthocyanin biosynthesis pathway is yet to be answered. Herein, we conduct an integrated analysis of transcriptomes and metabolome on fruits of two mulberry genotypes (‘Zijin’, ZJ, and ‘Dashi’, DS, with high and low anthocyanin abundance, respectively) at different post-flowering stages. In total, 1035 upregulated genes were identified in ZJ and DS, including MYBA in the MBW complex and anthocyanin related genes such as F3H. A KEGG analysis suggested that flavonoid biosynthesis and plant hormone signaling transduction pathways were significantly enriched in the upregulated gene list. In particular, among 103 ERF genes, the expression of ERF5 showed the most positive correlation with the anthocyanin change pattern across both genotypes and in the post-flowering stages, with a Pearson correlation coefficient (PCC) of 0.93. Electrophoresis mobility shift assay (EMSA) and luciferase assay suggested that ERF5 binds to the promoter regions of MYBA and F3H and transcriptionally activates their gene expression. We elucidated a potential mechanism by which ethylene enhances anthocyanin accumulation in mulberry fruits and highlighted the importance of the ERF5 gene in controlling the anthocyanin content in mulberry species. This knowledge could be used for engineering purposes in future mulberry breeding programs.
Chromatin loops (or chromatin interactions) are important elements of chromatin structures. Disruption of chromatin loops is associated with many diseases, such as cancer and polydactyly. A few methods, including ChIA-PET, HiChIP and PLAC-Seq, have been proposed to detect high-resolution, specific protein-mediated chromatin loops. With rapid progress in 3D genomic research, ChIA-PET, HiChIP and PLAC-Seq datasets continue to accumulate, and effective collection and processing for these datasets are urgently needed. Here, we developed a comprehensive, multispecies and specific protein-mediated chromatin loop database (ChromLoops, https://3dgenomics.hzau.edu.cn/chromloops), which integrated 1030 ChIA-PET, HiChIP and PLAC-Seq datasets from 13 species, and documented 1 491 416 813 high-quality chromatin loops. We annotated genes and regions overlapping with chromatin loop anchors with rich functional annotations, such as regulatory elements (enhancers, super-enhancers and silencers), variations (common SNPs, somatic SNPs and eQTLs), and transcription factor binding sites. Moreover, we identified genes with high-frequency chromatin interactions in the collected species. In particular, we identified genes with high-frequency interactions in cancer samples. We hope that ChromLoops will provide a new platform for studying chromatin interaction regulation in relation to biological processes and disease.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.