Genome-wide analysis of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes reveals a crucial role of the PIP subfamily in the water balance of laticifers

2016 ◽  
Keyword(s):  
Water Balance ◽  
Hevea Brasiliensis ◽  
Crucial Role ◽  
Rubber Tree ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

Planta ◽  
2012 ◽  
Vol 236 (2) ◽  
pp. 437-445 ◽  
Author(s):  
Manassawe Lertpanyasampatha ◽  
Lei Gao ◽  
Panida Kongsawadworakul ◽  
Unchera Viboonjun ◽  
Hervé Chrestin ◽  
...  
Keyword(s):  
High Throughput ◽  
Hevea Brasiliensis ◽  
High Throughput Sequencing ◽  
Rubber Tree ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-wide identification of lncRNAs, miRNAs, mRNAs, and their regulatory networks involved in tapping panel dryness in rubber tree (Hevea brasiliensis)

2021 ◽  
Author(s):  
Hui Liu ◽  
Yiyu Hu ◽  
Kun Yuan ◽  
Chengtian Feng ◽  
Qiguang He ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Regulatory Networks ◽  
Functional Characterization ◽  
Rubber Tree ◽  
Healthy Tree ◽  
Rubber Biosynthesis ◽  
Genome Wide ◽  
Tapping Panel Dryness

Abstract Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis) is largely unknown. Here, the whole transcriptomes of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNA (DEMs), genes (DEGs), and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs, and 1,574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. KEGG analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were down-regulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and two and 44 DELs were predicted as precursors and endogenous target mimics (eTMs) of two and six DEMs, respectively. Based on these, the DEL-DEM-DEG regulatory network involved in TPD was constructed, and 13 hub DELs, three hub DEMs and two hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of lncRNAs, miRNAs, and genes involved in TPD in rubber tree.

scholarly journals Cysteine-Rich Hydrophobin Gene Family: Genome Wide Analysis, Phylogeny and Transcript Profiling in Cordyceps militaris

2021 ◽  
Vol 22 (2) ◽  
pp. 643
Author(s):  
Xiao Li ◽  
Fen Wang ◽  
Yanyan Xu ◽  
Guijun Liu ◽  
Caihong Dong
Keyword(s):  
Life Cycle ◽  
Pathogenic Fungi ◽  
Class Ii ◽  
Cordyceps Militaris ◽  
Transcript Profiling ◽  
Saprotrophic Fungi ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Encoding Genes

Hydrophobins are a family of small secreted proteins found exclusively in fungi, and they play various roles in the life cycle. In the present study, genome wide analysis and transcript profiling of the hydrophobin family in Cordyceps militaris, a well-known edible and medicinal mushroom, were studied. The distribution of hydrophobins in ascomycetes with different lifestyles showed that pathogenic fungi had significantly more hydrophobins than saprotrophic fungi, and class II members accounted for the majority. Phylogenetic analysis of hydrophobin proteins from the species of Cordyceps s.l. indicated that there was more variability among the class II members than class I. Only a few hydrophobin-encoding genes evolved by duplication in Cordyceps s.l., which was inconsistent with the important role of gene duplication in basidiomycetes. Different transcript patterns of four hydrophobin-encoding genes during the life cycle indicated the possible different functions for each. The transcripts of Cmhyd2, 3 and 4 can respond to light and were related with the photoreceptors. CmQHYD, with four hydrophobin II domains, was first found in C. militaris, and multi-domain hydrophobins were only distributed in the species of Cordycipitaceae and Clavicipitaceae. These results could be helpful for further function research of hydrophobins and could provide valuable information for the evolution of hydrophobins.

Neuroinflammatory Signaling in the Pathogenesis of Alzheimer’s Disease

2021 ◽  
Vol 19 ◽  
Author(s):  
Md. Sahab Uddin ◽  
Md. Tanvir Kabir ◽  
Maroua Jalouli ◽  
Md. Ataur Rahman ◽  
Philippe Jeandet ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Innate Immune ◽  
Misfolded Proteins ◽  
Inflammatory Signaling ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Immunological Mechanisms ◽  
The Brain

: Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the formation of intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques. Growing evidence has suggested that AD pathogenesis is not only limited to the neuronal compartment but also strongly interacts with immunological processes in the brain. On the other hand, aggregated and misfolded proteins can bind with pattern recognition receptors located on astroglia and microglia and can in turn induce an innate immune response, characterized by the release of inflammatory mediators, ultimately playing a role in both the severity and the progression of the disease. It has been reported by genome-wide analysis that several genes which elevate the risk for sporadic AD encode for factors controlling the inflammatory response and glial clearance of misfolded proteins. Obesity and systemic inflammation are examples of external factors which may interfere with the immunological mechanisms of the brain and can induce disease progression. In this review, we discussed the mechanisms and essential role of inflammatory signaling pathways in AD pathogenesis. Indeed, interfering with immune processes and modulation of risk factors may lead to future therapeutic or preventive AD approaches.

scholarly journals Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Maria Victoria Gomez Roldan ◽  
Farhaj Izhaq ◽  
Marion Verdenaud ◽  
John Eleblu ◽  
Aimen Haraghi ◽  
...  
Keyword(s):  
Gene Networks ◽  
Growth Arrest ◽  
Reproductive Organs ◽  
Stress Signaling ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Inhibition Of Growth ◽  
Genome Wide ◽  
Male Flowers

AbstractIn cucurbits, CmWIP1 is a master gene controlling sex determination. To bring new insight in the function of CmWIP1, we investigated two Arabidopsis WIP transcription factors, AtWIP1/TT1 and AtWIP2/NTT. Using an inducible system we showed that WIPs are powerful inhibitor of growth and inducer of cell death. Using ChIP-seq and RNA-seq we revealed that most of the up-regulated genes bound by WIPs display a W-box motif, associated with stress signaling. In contrast, the down-regulated genes contain a GAGA motif, a known target of polycomb repressive complex. To validate the role of WIP proteins in inhibition of growth, we expressed AtWIP1/TT1 in carpel primordia and obtained male flowers, mimicking CmWIP1 function in melon. Using other promoters, we further demonstrated that WIPs can trigger growth arrest of both vegetative and reproductive organs. Our data supports an evolutionary conserved role of WIPs in recruiting gene networks controlling growth and adaptation to stress.

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