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https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#1
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29350309/population-genetics-of-the-endangered-and-wild-edible-plant-ottelia-acuminata-in-southwestern-china-using-novel-ssr-markers
#2
Shu Hua Zhai, Gen Shen Yin, Xiao Hong Yang
Ottelia acuminata is an edible aquatic plant species that is endemic to southwestern China. This plant has experienced habitat degradation resulting from environmental change and extensive human disturbance. Determining the genetic variation and genetic structure of O. acuminata populations could help develop strategies to collect, evaluate, utilize and conserve the species. To this end, we genotyped 183 individuals sampled throughout the species distribution using twelve novel nuclear microsatellite loci (nSSRs)...
January 19, 2018: Biochemical Genetics
https://www.readbyqxmd.com/read/29349608/comparative-transcriptomics-uncovers-differences-in-photoautotrophic-versus-photoheterotrophic-modes-of-nutrition-in-relation-to-secondary-metabolites-biosynthesis-in-swertia-chirayita
#3
Tarun Pal, Jibesh Kumar Padhan, Pawan Kumar, Hemant Sood, Rajinder S Chauhan
Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S...
January 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29348510/genome-and-secretome-analysis-of-pochonia-chlamydosporia-provide-new-insight-into-egg-parasitic-mechanisms
#4
Runmao Lin, Feifei Qin, Baoming Shen, Qianqian Shi, Chichuan Liu, Xi Zhang, Yang Jiao, Jun Lu, Yaoyao Gao, Marta Suarez-Fernandez, Federico Lopez-Moya, Luis Vicente Lopez-Llorca, Gang Wang, Zhenchuan Mao, Jian Ling, Yuhong Yang, Xinyue Cheng, Bingyan Xie
Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348240/snf1-related-kinase1-controlled-c-s1-bzip-signaling-activates-alternative-mitochondrial-metabolic-pathways-to-ensure-plant-survival-in-extended-darkness
#5
Lorenzo Pedrotti, Christoph Weiste, Thomas Nägele, Elmar Wolf, Francesca Lorenzin, Katrin Dietrich, Andrea Mair, Wolfram Weckwerth, Markus Teige, Elena Baena-González, Wolfgang Dröge-Laser
Sustaining energy homeostasis is of pivotal importance for all living organisms. In Arabidopsis thaliana, evolutionarily conserved SnRK1 kinases (Snf1-RELATED KINASE1) control metabolic adaptation during low energy stress. To unravel starvation-induced transcriptional mechanisms, we performed transcriptome studies of inducible knock-down lines and found that S1-basic leucine Zipper transcription factors (S1-bZIPs) control a defined subset of genes downstream of SnRK1. For example, S1-bZIPs coordinate the expression of genes involved in branched-chain amino acid catabolism, which constitutes an alternative mitochondrial respiratory pathway that is crucial for plant survival during starvation...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29347977/expansion-of-cytochrome-p450-and-cathepsin-genes-in-the-generalist-herbivore-brown-marmorated-stink-bug
#6
Raman Bansal, Andy Michel
BACKGROUND: The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29346685/metabolic-flux-engineering-of-cembratrien-ol-production-in-both-the-glandular-trichome-and-leaf-mesophyll-in-nicotiana-tabacum
#7
Hongying Zhang, Songtao Zhang, Yongxia Yang, Hongfang Jia, Hong Cui
Cembratrien-ol synthase (CBTS) catalyses the first step in cembranoid biosynthesis, producing cembratrien-ols in plant trichomes. In our previous study, microarray transcriptomes between leaves with trichomes and leaves without trichomes showed that a NtCBTS2 gene was expressed exclusively and abundantly in trichomes. Here, two NtCBTS2 isogenes (NtCBTS2a and NtCBTS2b), derived from a diploid genome donor, N. sylvestris, were identified from N. tabacum. Both genes were expressed primarily in trichomes, with relatively decreased transcription in flowers and stems, faint expression in roots, and no expression was detected in leaves lacking trichomes...
January 15, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#8
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29344874/laser-capture-microdissection-based-rna-seq-of-barley-grain-tissues
#9
Ronny Brandt, Martin Mascher, Johannes Thiel
Spatiotemporal patterning throughout the plant body depends to a large degree on cell- and tissue-specific expression of genes. Subsequently, for a better understanding of cell and tissue differentiation processes during plant development it is important to conduct transcript analyses in individual cells or tissue types rather than in bulk tissues. Laser capture microdissection (LCM) provides a useful method for isolating specific cell types from complex tissue structures for downstream applications. Contrasting to mammalian cells, the texture of plant cells is more critical due to hard, cellulose-rich cell walls, large vacuoles, and air spaces which complicates tissue preparation and extraction of macromolecules, like DNA and RNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344683/the-root-transcriptome-of-achyranthes-bidentata-and-the-identification-of-the-genes-involved-in-the-replanting-benefit
#10
Yan Hui Yang, Ming Jie Li, Yan Jie Yi, Rui Fang Li, Cheng Dong, Zhong Yi Zhang
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit...
January 17, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29343239/calcium-dependent-protein-kinases-in-cotton-insights-into-early-plant-responses-to-salt-stress
#11
Wei Gao, Fu-Chun Xu, Dan-Dan Guo, Jing-Ruo Zhao, Ji Liu, Ya-Wei Guo, Prashant Kumar Singh, Xiao-Nan Ma, Lu Long, Jose Ramon Botella, Chun-Peng Song
BACKGROUND: Soil salinization is one of the major environmental constraints to plant growth and agricultural production worldwide. Signaling components involving calcium (Ca2+) and the downstream calcium-dependent protein kinases (CPKs) play key roles in the perception and transduction of stress signals. However, the study of CPKs in cotton and their functions in response to salt stress remain unexplored. RESULTS: A total of 98 predicted CPKs were identified from upland cotton (Gossypium hirsutum L...
January 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29341868/transcriptional-evidence-for-crosstalk-between-ja-and-et-or-sa-during-root-knot-nematode-invasion-in-tomato
#12
Wenchao Zhao, Xiaoxuan Zhou, Hui Lei, Jingwei Fan, Rui Yang, Zilong Li, Canli Hu, Mengyan Li, Fukuan Zhao, Shaohui Wang
Previous studies have demonstrated that jasmonic acid (JA) reduces root-knot nematode (RKN) infections in tomato plants. RKN invasion is sensed by roots, and root-derived JA signaling activates systemic defense responses, though this is poorly understood. Here, we investigate variations in the RKN-induced transcriptome in scion phloem between two tomato plant grafts: CM/CM (Lycopersicum esculentum Mill. cv. Castlemart) and CM/spr2 (a JA-deficient mutant). A total of 8,716 genes were differentially expressed in the scion phloem of the plants with JA-deficient rootstock...
December 20, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/29340209/discovery-of-culex-pipiens-associated-tunisia-virus-a-new-ssrna-virus-representing-a-new-insect-associated-virus-family
#13
Diane Bigot, Célestine M Atyame, Mylène Weill, Fabienne Justy, Elisabeth A Herniou, Philippe Gayral
In the global context of arboviral emergence, deep sequencing unlocks the discovery of new mosquito-borne viruses. Mosquitoes of the species Culex pipiens, C. torrentium, and C. hortensis were sampled from 22 locations worldwide for transcriptomic analyses. A virus discovery pipeline was used to analyze the dataset of 0.7 billion reads comprising 22 individual transcriptomes. Two closely related 6.8 kb viral genomes were identified in C. pipiens and named as Culex pipiens associated tunisia virus (CpATV) strains Ayed and Jedaida...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29338737/transcriptome-profiling-of-whitefly-guts-in-response-to-tomato-yellow-leaf-curl-virus-infection
#14
Liang Geng, Li-Xin Qian, Ruo-Xuan Shao, Yin-Quan Liu, Shu-Sheng Liu, Xiao-Wei Wang
BACKGROUND: Plant viruses in agricultural crops are of great concern worldwide, and over 75% of them are transmitted from infected to healthy plants by insect vectors. Tomato yellow leaf curl virus (TYLCV) is a begomovirus, which is the largest and most economically important group of plant viruses, transmitted by the whitefly Bemisia tabaci. The circulation of TYLCV in the insect involves complex insect-virus interactions, whereas the molecular mechanisms of these interactions remain ambiguous...
January 16, 2018: Virology Journal
https://www.readbyqxmd.com/read/29338682/soybean-mads-box-gene-gmagl1-promotes-flowering-via-the-photoperiod-pathway
#15
Xuanrui Zeng, Hailun Liu, Hongyang Du, Sujing Wang, Wenming Yang, Yingjun Chi, Jiao Wang, Fang Huang, Deyue Yu
BACKGROUND: The MADS-box transcription factors are an ancient family of genes that regulate numerous physiological and biochemical processes in plants and facilitate the development of floral organs. However, the functions of most of these transcription factors in soybean remain unknown. RESULTS: In this work, a MADS-box gene, GmAGL1, was overexpressed in soybean. Phenotypic analysis showed that GmAGL1 overexpression not only resulted in early maturation but also promoted flowering and affected petal development...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338341/rna-sequencing-on-amomum-villosum-lour-induced-by-meja-identifies-the-genes-of-wrky-and-terpene-synthases-involved-in-terpene-biosynthesis
#16
Xueying He, Huan Wang, Jinfen Yang, Ke Deng, Teng Wang
Amomum villosum Lour. is an important Chinese medicine that has diverse medicinal functions, and mainly contains volatile terpenes This study aimed to explore the WRKY transcription factors (TFs) and terpene synthases (TPS) unigenes, which might be involved in terpene biosynthesis in A. villosum for providing some new information on the regulation of terpenes in plants. RNA sequencing of A.villosum-induced by methyl jasmonate (MeJA) revealed WRKY family was the second biggest TF family in the transcriptome...
January 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29338035/genome-wide-identification-of-wheat-and-brachypodium-type-one-protein-phosphatases-and-functional-characterization-of-durum-wheat-tdpp1a
#17
Mariem Bradai, Habib Mahjoubi, Andrea Chini, Marie-Edith Chabouté, Moez Hanin, Chantal Ebel
Reversible phosphorylation is an essential mechanism regulating signal transduction during development and environmental stress responses. An important number of dephosphorylation events in the cell are catalyzed by type one protein phosphatases (PP1), which catalytic activity is driven by the binding of regulatory proteins that control their substrate specificity or subcellular localization. Plants harbor several PP1 isoforms accounting for large functional redundancies. While animal PP1s were reported to play relevant roles in controlling multiple cellular processes, plant orthologs remain poorly studied...
2018: PloS One
https://www.readbyqxmd.com/read/29336199/the-rust-fungus-melampsora-larici-populina-expresses-a-conserved-genetic-program-and-distinct-sets-of-secreted-protein-genes-during-infection-of-its-two-host-plants-larch-and-poplar
#18
Cécile Lorrain, Clémence Marchal, Stéphane Hacquard, Christine Delaruelle, Jérémy Pétrowski, Benjamin Petre, Arnaud Hecker, Pascal Frey, Sebastien Duplessis
Mechanisms required for broad spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycles. Melampsora larici populina infects two taxonomically unrelated plants, larch on which sexual reproduction is achieved and poplar on which clonal multiplication occurs leading to severe epidemics in plantations. We applied deep RNA sequencing to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia and aecia; and we performed comparative transcriptomics of infection on poplar and larch hosts using available expression data...
January 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29335506/transcriptome-profiling-during-mangrove-viviparity-in-response-to-abscisic-acid
#19
Liwei Hong, Wenyue Su, Yuanye Zhang, Congting Ye, Yingjia Shen, Qingshun Q Li
Mangrove plants adapt to coastal tidal mudflats with specially evolved viviparity seed development. However, very little is known about the genetic and molecular mechanisms of mangrove viviparity. Here, we tested a hypothesis that plant hormone abscisic acid (ABA) plays a significant role in precocious germination of viviparous Kandelia obovata seeds by exogenous applications. Through transcriptome analysis of ABA treated seeds, it was found that ABA repressed mangrove fruit growth and development, and there were thousands of genes differentially expressed...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335449/transcriptome-profile-of-no-induced-arabidopsis-transcription-factor-genes-suggests-their-putative-regulatory-role-in-multiple-biological-processes
#20
Qari Muhammad Imran, Adil Hussain, Sang-Uk Lee, Bong-Gyu Mun, Noreen Falak, Gary J Loake, Byung-Wook Yun
TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis...
January 15, 2018: Scientific Reports
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