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https://www.readbyqxmd.com/read/28230761/transcriptomic-analysis-of-leaf-in-tree-peony-reveals-differentially-expressed-pigments-genes
#1
Jianrang Luo, Qianqian Shi, Lixin Niu, Yanlong Zhang
Tree peony (Paeonia suffruticosa Andrews) is an important traditional flower in China. Besides its beautiful flower, the leaf of tree peony has also good ornamental value owing to its leaf color change in spring. So far, the molecular mechanism of leaf color change in tree peony is unclear. In this study, the pigment level and transcriptome of three different color stages of tree peony leaf were analyzed. The purplish red leaf was rich in anthocyanin, while yellowish green leaf was rich in chlorophyll and carotenoid...
February 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#2
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28223999/factor-analysis-of-myb-gene-expression-and-flavonoid-affecting-petal-color-in-three-crabapple-cultivars
#3
Jie Zhang, Yingying Liu, YuFen Bu, Xi Zhang, Yuncong Yao
Flavonoid biosynthesis has received much attention concerning the structural genes and expression of the associated transcription factors (TFs). In the present study, we examined the gene expression patterns for petals of three colors using a statistical method. Factor analysis was successfully used to examine the expression patterns most present during regulation. The first expression patterns in the white and red petals were clearly demonstrated and have revealed different mechanisms of producing the proper components, whereas that in the pink petals was more complex, requiring factor analysis to supplement the other results...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28218758/variant-aware-saturating-mutagenesis-using-multiple-cas9-nucleases-identifies-regulatory-elements-at-trait-associated-loci
#4
Matthew C Canver, Samuel Lessard, Luca Pinello, Yuxuan Wu, Yann Ilboudo, Emily N Stern, Austen J Needleman, Frédéric Galactéros, Carlo Brugnara, Abdullah Kutlar, Colin McKenzie, Marvin Reid, Diane D Chen, Partha Pratim Das, Mitchel A Cole, Jing Zeng, Ryo Kurita, Yukio Nakamura, Guo-Cheng Yuan, Guillaume Lettre, Daniel E Bauer, Stuart H Orkin
Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants...
February 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28212614/transcriptomic-profiling-provides-molecular-insights-into-hydrogen-peroxide-induced-adventitious-rooting-in-mung-bean-seedlings
#5
Shi-Weng Li, Yan Leng, Rui-Fang Shi
BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212443/recurrent-rearrangements-of-the-myb-sant-like-dna-binding-domain-containing-3-gene-msantd3-in-salivary-gland-acinic-cell-carcinoma
#6
Nicholas Barasch, Xue Gong, Kevin A Kwei, Sushama Varma, Jewison Biscocho, Kunbin Qu, Nan Xiao, Joseph S Lipsick, Robert J Pelham, Robert B West, Jonathan R Pollack
Pathogenic gene fusions have been identified in several histologic types of salivary gland neoplasia, but not previously in acinic cell carcinoma (AcCC). To discover novel gene fusions, we performed whole-transcriptome sequencing surveys of three AcCC archival cases. In one specimen we identified a novel HTN3-MSANTD3 gene fusion, and in another a novel PRB3-ZNF217 gene fusion. The structure of both fusions was consistent with the promoter of the 5' partner (HTN3 or PRB3), both highly expressed salivary gland genes, driving overexpression of full-length MSANTD3 or ZNF217...
2017: PloS One
https://www.readbyqxmd.com/read/28210977/genetic-characterization-of-adenoid-cystic-carcinoma-of-the-minor-salivary-glands-a-potential-familial-occurrence-in-first-degree-relatives
#7
Hani Ibrahim Channir, Thomas van Overeem Hansen, Simon Andreasen, Christina Westmose Yde, Katalin Kiss, Birgitte Wittenborg Charabi
Adenoid cystic carcinoma (AdCC) is a malignant salivary gland tumor. To date, no cases of AdCC in first-degree relatives have been reported in the literature. We present a 50-year-old female (Case 1) and this patients' father (Case 2), both of whom were diagnosed with AdCC of the minor salivary glands. Histology of Case 1 demonstrated a tubulocribriform AdCC whereas Case 2 primarily was an AdCC of solid type. Both cases harbored the MYB-NFIB gene fusion as demonstrated by FISH and RNA-sequencing. After filtering and selection of putative deleterious variants, whole exome sequencing identified 18 germline variants in common between Case 1 and Case 2...
February 16, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/28209137/transcriptional-analysis-of-defense-mechanisms-in-upland-tetraploid-switchgrass-to-greenbugs
#8
Teresa Donze-Reiner, Nathan A Palmer, Erin D Scully, Travis J Prochaska, Kyle G Koch, Tiffany Heng-Moss, Jeffrey D Bradshaw, Paul Twigg, Keenan Amundsen, Scott E Sattler, Gautam Sarath
BACKGROUND: Aphid infestation of switchgrass (Panicum virgatum) has the potential to reduce yields and biomass quality. Although switchgrass-greenbug (Schizaphis graminum; GB) interactions have been studied at the whole plant level, little information is available on plant defense responses at the molecular level. RESULTS: The global transcriptomic response of switchgrass cv Summer to GB was monitored by RNA-Seq in infested and control (uninfested) plants harvested at 5, 10, and 15 days after infestation (DAI)...
February 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28199342/meta-qtl-for-resistance-to-white-mold-in-common-bean
#9
Renato C C Vasconcellos, O Blessing Oraguzie, Alvaro Soler, Haidar Arkwazee, James R Myers, Juan J Ferreira, Qijian Song, Phil McClean, Phillip N Miklas
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature)...
2017: PloS One
https://www.readbyqxmd.com/read/28198429/dynamic-changes-in-the-transcriptome-of-populus-hopeiensis-in-response-to-abscisic-acid
#10
Zhong Chen, Lexiang Ji, Jia Wang, Jinpu Jin, Xiaoyu Yang, Pian Rao, Kai Gao, Weihua Liao, Meixia Ye, Xinmin An
Abscisic acid (ABA) plays a fundamental role in plant response and adaptation to abiotic stresses, such as drought, high salinity and low temperature. Populus hopeiensis exhibits exceptional tolerance to water-deficit environments and is therefore an excellent choice for studying drought tolerance in trees. This study provides a global view of transcriptome dynamics in P. hopeiensis in response to exogenous ABA using Illumina RNA-sequencing. Endogenous ABA content increased and reached a peak at 8 h after ABA treatment and then significantly decreased at latter time points...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196843/changes-in-anthocyanin-production-during-domestication-of-citrus
#11
Eugenio Butelli, Andrés Garcia-Lor, Concetta Licciardello, Giuseppina Las Casas, Lionel Hill, Giuseppe Reforgiato Recupero, Manjunath Keremane, Chandrika Ramadugu, Robert Krueger, Qiang Xu, Xiuxin Deng, Anne-Laure Fanciullino, Yann Froelicher, Luis Navarro, Cathie Martin
Mandarin (C. reticulata), citron (C. medica) and pummelo (C. maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of citrus: sweet orange, sour orange, clementine, lemon, lime and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars...
February 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28174720/netrin-1-protects-hepatocytes-against-cell-death-through-sustained-translation-during-the-unfolded-protein-response
#12
Thomas Lahlali, Marie-Laure Plissonnier, Cristina Romero-López, Maud Michelet, Benjamin Ducarouge, Alfredo Berzal-Herranz, Fabien Zoulim, Patrick Mehlen, Romain Parent
BACKGROUND & AIMS: Netrin-1, a multifunctional secreted protein, is up-regulated in cancer and inflammation. Netrin-1 blocks apoptosis induced by the prototypical dependence receptors deleted in colorectal carcinoma and uncoordinated phenotype-5. Although the unfolded protein response (UPR) triggers apoptosis on exposure to stress, it first attempts to restore endoplasmic reticulum homeostasis to foster cell survival. Importantly, UPR is implicated in chronic liver conditions including hepatic oncogenesis...
May 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28167824/a-sugarcane-r2r3-myb-transcription-factor-gene-is-alternatively-spliced-during-drought-stress
#13
Jinlong Guo, Hui Ling, Jingjing Ma, Yun Chen, Yachun Su, Qingliang Lin, Shiwu Gao, Hengbo Wang, Youxiong Que, Liping Xu
MYB transcription factors of the R2R3-MYB family have been shown to play important roles in many plant processes. A sugarcane R2R3-MYB gene (ScMYB2) and its two alternative forms of transcript (ScMYB2S1 and ScMYB2S2) were identified in this study. The deduced protein of ScMYB2S1 is a typical plant R2R3-MYB protein, while ScMYB2S2 encodes a truncated protein. Real-time qPCR analysis revealed that ScMYB2S1 is suppressed under PEG-simulated drought stress in sugarcane, while ScMYB2S2 is induced at later treatment stage...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28167700/the-transcription-factor-myb29-is-a-regulator-of-alternative-oxidase-1
#14
Xinhua Zhang, Aneta Ivanova, Klaas Vandepoele, Jordan D Radomiljac, Jan Van de Velde, Oliver Berkowitz, Patrick Willems, Yue Xu, Sophia Ng, Olivier Van Aken, Owen Duncan, Botao Zhang, Véronique Storme, Kai Xun Chan, Dries Vaneechoutte, Barry J Pogson, Frank Van Breusegem, James Whelan, Inge De Clercq
Plants sense and integrate a variety of signals from the environment through various interacting signal transduction pathways that involve hormones and signaling molecules. Using the ALTERNATIVE OXIDASE 1a (AOX1a) gene expression as a model system of retrograde or stress signaling between mitochondria and the nucleus, the MYB DOMAIN PROTEIN 29 (MYB29) was identified as a negative regulator (rao7 mutant) in a genetic screen of Arabidopsis thaliana. rao7/myb29 mutants have increased levels of AOX1a at a transcript and protein level after induction with antimycin A...
February 6, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28167273/mybs-affect-the-variation-in-the-ratio-of-anthocyanin-and-flavanol-in-fruit-peel-and-flesh-in-response-to-shade
#15
Yanfen Lu, Yufen Bu, Suxiao Hao, Yaru Wang, Jie Zhang, Ji Tian, Yuncong Yao
Fruit pigment accumulation, which represents an important indicator of nutrient quality and appearance value, is often affected by low light under rain, cloud, fog and haze conditions during the veraison period. It is not known whether continuous low light interferes with the production and accumulation of secondary metabolites in veraison fruit. In this paper, we measured pigments and the transcriptional level of genes related to secondary metabolites, i.e., flavonoid biosynthesis in the peel and flesh of Malus crabapple 'Radiant' fruit in response to normal light and shade from 10th July to 30th August...
January 31, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28166404/vcbbx-vcmyb21-and-vcr2r3myb-transcription-factors-are-involved-in-uv-b-induced-anthocyanin-biosynthesis-in-the-peel-of-harvested-blueberry-fruit
#16
Chau T T Nguyen, Sooyeon Lim, Jeong Gu Lee, Eun Jin Lee
This study was carried out to better understand the mechanism responsible for increasing the anthocyanins in blueberries after UV-B radiation at 6.0 kJ m(-2) for 20 min. UV-B induced upregulation of genes involved in anthocyanin biosynthesis in blueberry fruit compared to a nontreated control. Phenylalanine ammonia lyase, chalcone synthase, and flavanone 3'-hydroxylase, which are enzymes that function upstream of anthocyanin biosynthesis, were significantly expressed by UV-B. Expression levels of VcBBX, VcMYB21, and VcR2R3MYB transcription factors (TFs) were upregulated by UV-B in the same manner as the anthocyanin biosynthesis genes...
February 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28165059/combined-analysis-of-mrna-and-mirna-identifies-dehydration-and-salinity-responsive-key-molecular-players-in-citrus-roots
#17
Rangjin Xie, Jin Zhang, Yanyan Ma, Xiaoting Pan, Cuicui Dong, Shaoping Pang, Shaolan He, Lie Deng, Shilai Yi, Yongqiang Zheng, Qiang Lv
Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28164785/functions-of-the-magnaporthe-oryzae-flb3p-and-flb4p-transcription-factors-in-the-regulation-of-conidiation
#18
S Matheis, A Yemelin, D Scheps, K Andresen, S Jacob, E Thines, A J Foster
The Magnaporthe oryzae genes FLB3 and FLB4, orthologues of the Aspergillus nidulans regulators of conidiation FlbC and FlbD, were inactivated. These genes encode C2H2 zinc finger and Myb-like transcription factors, respectively, in A. nidulans. Analysis of the resultant mutants demonstrated that FLB4 is essential for spore formation and that strains lacking this gene are fluffy in their colony morphology due to an inability to complete conidiophore formation. Meanwhile, FLB3 is required for normal levels of aerial mycelium formation...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28163714/transcriptomics-analysis-of-apple-leaves-in-response-to-alternaria-alternata-apple-pathotype-infection
#19
Longming Zhu, Weichen Ni, Shuai Liu, Binhua Cai, Han Xing, Sanhong Wang
Alternaria blotch disease of apple (Malus × domestica Borkh.), caused by the apple pathotype of Alternaria alternata, is one of the most serious fungal diseases to affect apples. To develop an understanding of how apples respond to A. alternata apple pathotype (AAAP) infection, we examined the host transcript accumulation over the period between 0 and 72 h post AAAP inoculation. Large-scale gene expression analysis was conducted of the compatible interaction between "Starking Delicious" apple cultivar and AAAP using RNA-Seq and digital gene expression (DGE) profiling methods...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28161858/wheat-drought-responsive-wxpl-transcription-factors-regulate-cuticle-biosynthesis-genes
#20
Huihui Bi, Sukanya Luang, Yuan Li, Natalia Bazanova, Nikolai Borisjuk, Maria Hrmova, Sergiy Lopato
The cuticle forms a hydrophobic waxy layer that covers plant organs and provides protection from biotic and abiotic stresses. Transcription of genes responsible for cuticle formation is regulated by several types of transcription factors (TFs). Five orthologous to WAX PRODUCTION (WXP1 and WXP2) genes from Medicago truncatula were isolated from a cDNA library prepared from flag leaves and spikes of drought tolerant wheat (Triticum aestivum, breeding line RAC875) and designated TaWXP-like (TaWXPL) genes. Tissue-specific and drought-responsive expression of TaWXPL1D and TaWXPL2B was investigated by quantitative RT-PCR in two Australian wheat genotypes, RAC875 and Kukri, with contrasting glaucousness and drought tolerance...
February 4, 2017: Plant Molecular Biology
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