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1. A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis

Author:
Nibert, MaxL.; Manny, AustinR.; Debat, HumbertoJ.; Firth, AndrewE.; Bertini, Laura; Caruso, Carla
Source:
Archives of virology 2018 v.163 no.7 pp. 1921-1926
ISSN:
0304-8608
Subject:
transcriptome,   etc   ; Barnavirus; Colobanthus quitensis; RNA; RNA-directed RNA polymerase; coat proteins; databases; fungi; open reading frames; polyproteins; translation (genetics); viruses; Antarctic region;     Show all 13 Subjects
Abstract:
... Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as ...
DOI:
10.1007/s00705-018-3794-x
PubMed:
29516246
PubMed Central:
PMC5999160

2. Acclimation-induced metabolic reprogramming contributes to rapid desiccation tolerance acquisition in Boea hygrometrica

Author:
Sun, Run-Ze; Lin, Chih-Ta; Zhang, Xiao-Fei; Duan, Li-Xin; Qi, Xiao-Quan; Gong, Yue-Hua; Deng, Xin
Source:
Environmental and experimental botany 2018 v.148 pp. 70-84
ISSN:
0098-8472
Subject:
transcriptome,   etc   ; abscisic acid; acclimation; alpha-tocopherol; biomarkers; biosynthesis; carbon; discriminant analysis; drought; drought tolerance; energy metabolism; enzymes; fatty acids; gas chromatography-mass spectrometry; glutaric acid; least squares; leaves; maltose; messenger RNA; metabolites; multigene family; rehydration; signal transduction; transcription (genetics); tryptophan; ubiquitination;     Show all 26 Subjects
Abstract:
... The acquisition of rapid desiccation tolerance for the resurrection plant Boea hygrometrica requires a cycle of drought acclimation. Here, a gas chromatography-mass spectrometry based global untargeted metabolite profiling analysis was conducted on leaves of B. hygrometrica during dehydration and rehydration. Metabolic profiles between non-acclimated and drought acclimated plants were clearly dist ...
DOI:
10.1016/j.envexpbot.2018.01.008

3. Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR

Author:
Walton, Zandra E.; Patel, Chirag H.; Brooks, Rebekah C.; Yu, Yongjun; Ibrahim-Hashim, Arig; Riddle, Malini; Porcu, Alessandra; Jiang, Tianying; Ecker, Brett L.; Tameire, Feven; Koumenis, Constantinos; Weeraratna, Ashani T.; Welsh, David K.; Gillies, Robert; Alwine, James C.; Zhang, Lin; Powell, Jonathan D.; Dang, Chi V.
Source:
Cell 2018 v.174 no.1 pp. 72-87.e32
ISSN:
0092-8674
Subject:
transcriptome,   etc   ; T-lymphocytes; acidification; biochemical pathways; cell lines; circadian clocks; circadian rhythm; genes; humans; hypoxia; lactic acid; lysosomes; mice; models; rapamycin; transcription (genetics);     Show all 16 Subjects
Abstract:
... Recent reports indicate that hypoxia influences the circadian clock through the transcriptional activities of hypoxia-inducible factors (HIFs) at clock genes. Unexpectedly, we uncover a profound disruption of the circadian clock and diurnal transcriptome when hypoxic cells are permitted to acidify to recapitulate the tumor microenvironment. Buffering against acidification or inhibiting lactic acid ...
DOI:
10.1016/j.cell.2018.05.009

4. A comparative study of three akirin genes from big belly seahorse Hippocampus abdominalis: Molecular, transcriptional and functional characterization

Author:
Pavithiran, Amirthalingam; Bathige, S.D.N.K.; Kugapreethan, Roopasingam; Priyathilaka, Thanthrige Thiunuwan; Yang, Hyerim; Kim, Myoung-Jin; Lee, Jehee
Source:
Fish & shellfish immunology 2018 v.74 pp. 584-592
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Hippocampus abdominalis; Streptococcus iniae; carcinogenesis; cytoplasm; databases; embryogenesis; enzyme activity; fish; gene expression; genes; immunity; kidneys; liver; luciferase; muscle development; nuclear localization signals; nuclear proteins; pathogens; phylogeny; polyinosinic-polycytidylic acid; shellfish; signal transduction; tissues; transcription (genetics); transcription factor NF-kappa B;     Show all 26 Subjects
Abstract:
... Akirins, members of the NF-κB signaling pathway, are highly conserved nuclear proteins, which regulate gene expression in many physiological processes, including immunity, myogenesis, carcinogenesis, and embryogenesis. The akirin family in teleost fish consists of two to three genes. In the present study, three akirin genes from Hippocampus abdominalis were identified from a transcriptome database ...
DOI:
10.1016/j.fsi.2018.01.025

5. A comparative transcriptome approach for identification of molecular changes in Aphanomyces invadans infected Channa striatus

Author:
Kumaresan, Venkatesh; Pasupuleti, Mukesh; Arasu, Mariadhas Valan; Al-Dhabi, Naif Abdullah; Arshad, Aziz; Amin, S. M. Nurul; Yusoff, Fatimah Md.; Arockiaraj, Jesu
Source:
Molecular biology reports 2018 v.45 no.6 pp. 2511-2523
ISSN:
0301-4851
Subject:
transcriptome,   etc   ; Aphanomyces; Channa striata; RNA; epizootic diseases; fish; fungi; gene expression regulation; genes; immune response; immunoglobulins; pathogens; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; Asia;     Show all 15 Subjects
Abstract:
... Snakehead murrel, Channa striatus is an economically important aquatic species in Asia and are widely cultured and captured because of its nutritious and medicinal values. Their growth is predominantly affected by epizootic ulcerative syndrome (EUS) which is primarily caused by an oomycete fungus, Aphanomyces invadans. However, the molecular mechanism of immune response in murrel against this infe ...
DOI:
10.1007/s11033-018-4418-y

6. A comparative transcriptomic approach to understanding the formation of cork

Author:
Boher, Pau; Soler, Marçal; Sánchez, Anna; Hoede, Claire; Noirot, Céline; Paiva, JorgeAlmiro Pinto; Serra, Olga; Figueras, Mercè
Source:
Plant molecular biology 2018 v.96 no.1-2 pp. 103-118
ISSN:
0167-4412
Subject:
transcriptome,   etc   ; Quercus ilex; Quercus suber; abiotic stress; bark; cambium; chromatin; cork; gene expression regulation; metabolism; ontogeny; periderm; regulator genes; secondary phloem; suberin; transcriptomics; wood;     Show all 17 Subjects
Abstract:
... KEY MESSAGE: The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer ba ...
DOI:
10.1007/s11103-017-0682-9

7. A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells

Author:
Frahm, Krystle A.; Waldman, Jacob K.; Luthra, Soumya; Rudine, Anthony C.; Monaghan-Nichols, A. Paula; Chandran, Uma R.; DeFranco, Donald B.
Source:
Molecular and cellular endocrinology 2018 v.471 pp. 42-50
ISSN:
0303-7207
Subject:
transcriptome,   etc   ; brain; data collection; dexamethasone; embryo (animal); females; gene expression; gene expression regulation; genes; glucocorticoids; males; mice; neural networks; sequence analysis; sexual dimorphism; stem cells; synthetic glucocorticoids;     Show all 17 Subjects
Abstract:
... Fetal exposure to synthetic glucocorticoids reprograms distinct neural circuits in the developing brain, often in a sex-specific manner, via mechanisms that remain poorly understood. To reveal whether such reprogramming is associated with select molecular signatures, we characterized the transcriptome of primary, embryonic mouse cerebral cortical and hypothalamic neural progenitor/stem cells deriv ...
DOI:
10.1016/j.mce.2017.05.026

8. Actinidia-Pseudomonas syringae pv. actinidiae interaction: differentially expressed plant transcripts during infection

Author:
Michelotti, V.; Lamontanara, A.; Orrù, L.; Cellini, A.; Donati, I.; Buriani, G.; Vanneste, J. L.; Cattivelli, L.; Spinelli, F.; Tacconi, G.
Source:
Acta horticulturae 2018 no.1218 pp. 315-320
ISSN:
0567-7572
Subject:
transcriptome,   etc   ; Actinidia chinensis; Pseudomonas syringae pv. actinidiae; acibenzolar-S-methyl; bacterial canker; genes; kiwifruit; messenger RNA; pandemic; transcription (genetics); transcription factors;     Show all 11 Subjects
Abstract:
... Since 2008, kiwifruit bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has spread to pandemic scale. In order to elucidate the molecular events of the kiwifruit-Psa interaction, Illumina RNAseq was conducted after Psa inoculation and mock inoculation, on both acibenzolar-S-methyl (ASM) treated and untreated Actinidia chinensis plants. De-novo assembly of the kiwifruit transcrip ...
DOI:
10.17660/ActaHortic.2018.1218.43

9. Activation of a gene network in durum wheat roots exposed to cadmium

Author:
Aprile, Alessio; Sabella, Erika; Vergine, Marzia; Genga, Alessandra; Siciliano, Maria; Nutricati, Eliana; Rampino, Patrizia; De Pascali, Mariarosaria; Luvisi, Andrea; Miceli, Antonio; Negro, Carmine; De Bellis, Luigi
Source:
BMC plant biology 2018 v.18 no.1 pp. 238
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Triticum turgidum subsp. durum; biomass; biosynthesis; cadmium; crops; cultivars; durum wheat; farmers; gene expression regulation; genes; heavy metals; human health; hydroponics; international trade; methionine; nicotianamine; phytosiderophores; phytotoxicity; polluted soils; risk; roots; sequence analysis; shoots; tissues; transcription factors; transcriptomics; transporters; vacuoles;     Show all 29 Subjects
Abstract:
... BACKGROUND: Among cereals, durum wheat (Triticum turgidum L. subsp. durum) accumulates cadmium (Cd) at higher concentration if grown in Cd-polluted soils. Since cadmium accumulation is a risk for human health, the international trade organizations have limited the acceptable concentration of Cd in edible crops. Therefore, durum wheat cultivars accumulating low cadmium in grains should be preferred ...
DOI:
10.1186/s12870-018-1473-4

10. Acute hypoxia stress induced abundant differential expression genes and alternative splicing events in heart of tilapia

Author:
Xia, Jun Hong; Li, Hong Lian; Li, Bi Jun; Gu, Xiao Hui; Lin, Hao Ran
Source:
Gene 2018 v.639 pp. 52-61
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; Oreochromis niloticus; RNA-binding proteins; alternative splicing; aquatic environment; brain; data collection; energy conservation; enzyme activity; exons; fish; gene expression; genes; gills; glycolysis; heart; hypoxia; immune response; liver; oxidative stress; protein synthesis; ribosomal proteins; ribosomes; sequence analysis; spleen; transcriptomics;     Show all 26 Subjects
Abstract:
... Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expre ...
DOI:
10.1016/j.gene.2017.10.002

11. Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri

Author:
Schvartzman, M. Sol; Corso, Massimiliano; Fataftah, Nazeer; Scheepers, Maxime; Nouet, Cécile; Bosman, Bernard; Carnol, Monique; Motte, Patrick; Verbruggen, Nathalie; Hanikenne, Marc
Source:
Thenew phytologist 2018 v.218 no.1 pp. 269-282
ISSN:
0028-646X
Subject:
transcriptome,   etc   ; Arabidopsis halleri; atomic absorption spectrometry; gene expression; hyperaccumulators; ionomics; iron; nutrient deficiencies; phenotype; polluted soils; provenance; roots; sequence analysis; shoots; tissues; transcriptomics; zinc; Italy; Poland;     Show all 19 Subjects
Abstract:
... Zinc (Zn) hyperaccumulation and hypertolerance are highly variable traits in Arabidopsis halleri. Metallicolous populations have evolved from nearby nonmetallicolous populations in multiple independent adaptation events. To determine whether these events resulted in similar or divergent adaptive strategies to high soil Zn concentrations, we compared two A. halleri metallicolous populations from di ...
DOI:
10.1111/nph.14949

12. Adaptively differential expression analysis in gill of Chinese mitten crabs (Eriocheir japonica sinensis) associated with salinity changes

Author:
Zhang, Daizhen; Qi, Tingting; Liu, Jun; Liu, Qiuning; Jiang, Senhao; Zhang, Huabin; Wang, Zhengfei; Ding, Ge; Tang, Boping
Source:
International journal of biological macromolecules 2018 v.120 pp. 2242-2246
ISSN:
0141-8130
Subject:
transcriptome,   etc   ; Eriocheir sinensis; H-transporting ATP synthase; acid-base balance; aquaculture; biomarkers; body fluids; desalination; excretion; freshwater; gene expression regulation; genes; gills; habitats; hemolymph; life history; marine environment; nitrogen; osmolality; osmoregulation; quantitative polymerase chain reaction; salinity; sodium; China;     Show all 24 Subjects
Abstract:
... Desalination of marine species has become an important development direction for aquaculture in China and other countries. However, that how to regulate the salt balance to adapt to new freshwater habitats is a serious challenge for marine species in desalination of aquaculture. In the study, Chinese mitten crabs (Eriocheir japonica sinensis) was selected to analyse the adaptively differential exp ...
DOI:
10.1016/j.ijbiomac.2018.08.054

13. Adaptive response of pearl oyster Pinctada fucata martensii to low water temperature stress

Author:
Wang, Qingheng; Liu, Ya; Zheng, Zhe; Deng, Yuewen; Jiao, Yu; Du, Xiaodong
Source:
Fish & shellfish immunology 2018 v.78 pp. 310-315
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; Pinctada fucata; amino acid metabolism; amino acids; biosynthesis; cold stress; cold zones; energy; gene expression regulation; genes; immunity; lysosomes; models; oxidative phosphorylation; oysters; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; shellfish; transcriptomics; unsaturated fatty acids; water temperature;     Show all 22 Subjects
Abstract:
... The pearl oyster Pinctada fucata martensii is a warm-water shellfish that is sensitive to cold environments. To investigate its potential adaptation to low-temperature stress, the selected line (SL) and based population (BP) were sampled to undergo transcriptome sequence. Results of transcriptome analysis showed 572 significant differentially expressed genes. The typical HSP70 and HSP40 exhibited ...
DOI:
10.1016/j.fsi.2018.04.049

14. A deep insight into the male and female sialotranscriptome of adult Culex tarsalis mosquitoes

Author:
Ribeiro, José M.C.; Martin-Martin, Ines; Moreira, Fernando R.; Bernard, Kristen A.; Calvo, Eric
Source:
Insect biochemistry and molecular biology 2018 v.95 pp. 1-9
ISSN:
0965-1748
Subject:
transcriptome,   etc   ; Culex tarsalis; adults; apyrase; expressed sequence tags; females; hematophagy; males; prices; salivary glands; sequence analysis; sugar feeding;     Show all 12 Subjects
Abstract:
... Previously, a Sanger-based sialotranscriptome analysis of adult female Culex tarsalis was published based on ∼2000 ESTs. During the elapsed 7.5 years, pyrosequencing has been discontinued and Illumina sequences have increased considerable in size and decreased in price. We here report an Illumina-based sialotranscriptome that allowed finding the missing apyrase from the salivary transcriptome of C ...
DOI:
10.1016/j.ibmb.2018.03.001

15. A 1-deoxy-d-xylulose 5-phosphate reductoisomerase gene probably involved in the synthesis of terpenoids in Chrysanthemum indicum var. aromaticum

Author:
Gao, Wenjie; Wang, Xiang; Purente, Nuananong; Muhammad, Luqman; Zhou, Yunwei; He, Miao
Source:
Canadian journal of plant science 2018 v.98 no.6 pp. 1254-1264
ISSN:
1918-1833
Subject:
transcriptome,   etc   ; Chrysanthemum indicum; alcohol oxidoreductases; amino acids; bioinformatics; elicitors; genes; leaves; messenger RNA; metabolism; methyl jasmonate; ornamental plants; physicochemical properties; polypeptides; quantitative polymerase chain reaction; secondary metabolites; secretion; terpenoids;     Show all 18 Subjects
Abstract:
... Terpenoids are important secondary metabolites in plants. The synthesis of terpenoids involves a key enzyme, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR). In an aromatic ornamental plant, Chrysanthemum indicum var. aromaticum, terpenoids were found to be an important component in leaf secretions. To study the regulatory mechanism of terpenoid synthesis in C. indicum var. aromaticum, we cl ...
DOI:
10.1139/cjps-2017-0070

16. A dominant‐interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana

Author:
Jacob, Florence; Kracher, Barbara; Mine, Akira; Seyfferth, Carolin; Blanvillain‐Baufumé, Servane; Parker, Jane E.; Tsuda, Kenichi; Schulze‐Lefert, Paul; Maekawa, Takaki
Source:
Thenew phytologist 2018 v.217 no.4 pp. 1667-1680
ISSN:
0028-646X
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; barley; cell death; data collection; disease resistance; gene induction; genes; immune response; immunologic receptors; loci; mutants; mutation; pathogen-associated molecular patterns; pathogens; plant hormones; transcription (genetics); transgenic plants;     Show all 18 Subjects
Abstract:
... Pattern recognition receptors (PRRs) and nucleotide‐binding domain and leucine‐rich repeat (LRR)‐containing proteins (NLRs) initiate pattern‐triggered immunity (PTI) and effector‐triggered immunity (ETI), respectively, each associated with the activation of an overlapping set of defence genes. The regulatory mechanism behind this convergence of PTI‐ and ETI‐mediated defence gene induction remains ...
DOI:
10.1111/nph.14943
PubMed:
29226970
PubMed Central:
PMC5873390

17. Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis

Author:
Osman, Kim; Yang, Jianhua; Roitinger, Elisabeth; Lambing, Christophe; Heckmann, Stefan; Howell, Elaine; Cuacos, Maria; Imre, Richard; Dürnberger, Gerhard; Mechtler, Karl; Armstrong, Susan; Franklin, F. Christopher H.
Source:
The plant journal 2018 v.93 no.1 pp. 17-33
ISSN:
0960-7412
Subject:
transcriptome,   etc   ; Arabidopsis; Brassica oleracea; DNA replication; anthers; chromosome segregation; chromosomes; genes; genetic variation; meiosis; mutants; phosphorylation; prophase; protein-protein interactions; proteins; proteolysis; proteome; proteomics;     Show all 18 Subjects
Abstract:
... During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functiona ...
DOI:
10.1111/tpj.13752

18. A foreleg transcriptome for Ixodes scapularis ticks: Candidates for chemoreceptors and binding proteins that might be expressed in the sensory Haller’s organ

Author:
Josek, Tanya; Walden, Kimberly K.O.; Allan, Brian F.; Alleyne, Marianne; Robertson, Hugh M.
Source:
Ticks and tick-borne diseases 2018 v.9 no.5 pp. 1317-1327
ISSN:
1877-959X
Subject:
transcriptome,   etc   ; Ixodes scapularis; binding proteins; chemoreceptors; gene expression regulation; genes; glutamate receptors; insects; legs; odor compounds; protein secretion; smell; taste; tick-borne diseases; ticks;     Show all 15 Subjects
Abstract:
... Little is known about the molecular basis for the olfactory capabilities of the sensory Haller’s organ on the forelegs of ticks. We first expanded the known repertoire of Ionotropic Receptors (IRs), a variant lineage of the ionotropic glutamate receptors, encoded by the black-legged Ixodes scapularis genome from 15 to 125. We then undertook a transcriptome study of fore- and hind-legs of this tick ...
DOI:
10.1016/j.ttbdis.2018.05.013

19. A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates

Author:
Neumann, Anthony P.; Weimer, Paul J.; Suen, Garret
Source:
Biotechnology for biofuels 2018 v.11 no.1 pp. 295
ISSN:
1754-6834
Subject:
transcriptome,   etc   ; Fibrobacter succinogenes; anaerobes; bacteria; biofuels; biopolymers; carbohydrate binding; cattle; cellobiose; cellulose; economics; endo-1,4-beta-glucanase; fermented foods; gene expression; genes; glucose; hemicellulose; hydrolysis; plankton; rumen;     Show all 20 Subjects
Abstract:
... BACKGROUND: Cellulose is the most abundant biological polymer on earth, making it an attractive substrate for the production of next-generation biofuels and commodity chemicals. However, the economics of cellulose utilization are currently unfavorable due to a lack of efficient methods for its hydrolysis. Fibrobacter succinogenes strain S85, originally isolated from the bovine rumen, is among the ...
DOI:
10.1186/s13068-018-1290-x
CHORUS:
10.1186/s13068-018-1290-x

20. A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation

Author:
Wang, Maojun; Wang, Pengcheng; Liang, Fan; Ye, Zhengxiu; Li, Jianying; Shen, Chao; Pei, Liuling; Wang, Feng; Hu, Jiang; Tu, Lili; Lindsey, Keith; He, Daohua; Zhang, Xianlong
Source:
The new phytologist 2018 v.217 no.1 pp. 163-178
ISSN:
0028-646X
Subject:
transcriptome,   etc   ; DNA methylation; allopolyploidy; alternative splicing; cotton; eukaryotic cells; exons; genes; high-throughput nucleotide sequencing; microRNA; models; nucleosomes; sequence homology; surveys;     Show all 14 Subjects
Abstract:
... Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high‐throughput next‐generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity be ...
DOI:
10.1111/nph.14762

21. AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

Author:
Robinson, Andrew J.; Tamiru, Muluneh; Salby, Rachel; Bolitho, Clayton; Williams, Andrew; Huggard, Simon; Fisch, Eva; Unsworth, Kathryn; Whelan, James; Lewsey, Mathew G.
Source:
BMC plant biology 2018 v.18 no.1 pp. 200
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Arabidopsis; barley; bioinformatics; cooperative research; corn; crops; data collection; databases; developmental stages; experts; genes; genomics; rice; sequence analysis; tissues; tomatoes; wheat;     Show all 18 Subjects
Abstract:
... BACKGROUND: The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However ...
DOI:
10.1186/s12870-018-1406-2

22. A head transcriptome provides insights into odorant binding proteins of the bamboo grasshopper

Author:
Li, Ran; Jiang, Guo-Fang; Dong, Si-Yu
Source:
Genes & genomics 2018 v.40 no.9 pp. 991-1000
ISSN:
1976-9571
Subject:
transcriptome,   etc   ; antennae; bamboos; binding proteins; databases; ecology; genes; genomics; grasshoppers; head; high-throughput nucleotide sequencing; odor compounds; pests; protocols; reverse transcriptase polymerase chain reaction; semiochemicals; tissue distribution; tissues; transcriptomics; China;     Show all 20 Subjects
Abstract:
... The bamboo grasshopper Ceracris kiangsu is a famous bamboo pest in China. The identification of genes involved in olfactory behavior of C. kiangsu is necessary for better understanding the molecular basis and expression profiles of behavior ecology. However, necessary genomic and transcriptomic data are lacking in the species, limiting control efficiency. The primary objective of this study was to ...
DOI:
10.1007/s13258-018-0706-0

23. A high parasite density environment induces transcriptional changes and cell death in Plasmodium falciparum blood stages

Author:
Chou, Evelyn S.; Abidi, Sabia Z.; Teye, Marian; Leliwa‐Sytek, Aleksandra; Rask, Thomas S.; Cobbold, Simon A.; Tonkin‐Hill, Gerry Q.; Subramaniam, Krishanthi S.; Sexton, Anna E.; Creek, Darren J.; Daily, Johanna P.; Duffy, Michael F.; Day, Karen P.
Source:
The FEBS journal 2018 v.285 no.5 pp. 848-870
ISSN:
1742-464X
Subject:
transcriptome,   etc   ; Plasmodium falciparum; antigenic variation; apoptosis; databases; death; erythrocytes; gene expression; gene expression regulation; genes; glucose; immunity; lactic acid; malaria; mammals; membrane potential; merozoites; metabolism; mitochondrial membrane; parasites; phenotype; population size; schizonts; starvation; transcription (genetics); yeasts;     Show all 26 Subjects
Abstract:
... Transient regulation of Plasmodium numbers below the density that induces fever has been observed in chronic malaria infections in humans. This species transcending control cannot be explained by immunity alone. Using an in vitro system we have observed density dependent regulation of malaria population size as a mechanism to possibly explain these in vivo observations. Specifically, Plasmodium fa ...
DOI:
10.1111/febs.14370

24. A high-resolution map of the human small non-coding transcriptome

Author:
Fehlmann, Tobias; Backes, Christina; Alles, Julia; Fischer, Ulrike; Hart, Martin; Kern, Fabian; Langseth, Hilde; Rounge, Trine; Umu, Sinan Ugur; Kahraman, Mustafa; Laufer, Thomas; Haas, Jan; Staehler, Cord; Ludwig, Nicole; Hübenthal, Matthias; Meder, Benjamin; Franke, Andre; Lenhof, Hans-Peter; Meese, Eckart; Keller, Andreas; Birol, Inanc
Source:
Bioinformatics 2018 v.34 no.10 pp. 1621-1628
ISSN:
1460-2059
Subject:
transcriptome,   etc   ; bioinformatics; data collection; genome; humans; lung neoplasms; microRNA; non-coding RNA; sequence analysis;     Show all 9 Subjects
Abstract:
... Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome. In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On ...
DOI:
10.1093/bioinformatics/btx814

25. Air pollution and the fetal origin of disease: A systematic review of the molecular signatures of air pollution exposure in human placenta

Author:
Luyten, Leen J.; Saenen, Nelly D.; Janssen, Bram G.; Vrijens, Karen; Plusquin, Michelle; Roels, Harry A.; Debacq-Chainiaux, Florence; Nawrot, Tim S.
Source:
Environmental research 2018 v.166 pp. 310-323
ISSN:
0013-9351
Subject:
transcriptome,   etc   ; air; air pollution; biomarkers; databases; fetal development; fetus; genome; genomics; humans; maternal exposure; metabolism; metabolomics; placenta; pregnancy; proteome; proteomics; systematic review; transcriptomics;     Show all 19 Subjects
Abstract:
... Fetal development is a crucial window of susceptibility in which exposure-related alterations can be induced on the molecular level, leading to potential changes in metabolism and development. The placenta serves as a gatekeeper between mother and fetus, and is in contact with environmental stressors throughout pregnancy. This makes the placenta as a temporary organ an informative non-invasive mat ...
DOI:
10.1016/j.envres.2018.03.025

26. A key structural gene, AaLDOX, is involved in anthocyanin biosynthesis in all red-fleshed kiwifruit (Actinidia arguta) based on transcriptome analysis

Author:
Li, Yukuo; Fang, Jinbao; Qi, Xiujuan; Lin, Miaomiao; Zhong, Yunpeng; Sun, Leiming
Source:
Gene 2018 v.648 pp. 31-41
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; Actinidia arguta; Actinidia chinensis; anthocyanins; biochemical pathways; biosynthesis; cluster analysis; color; cultivars; gene expression regulation; kiwifruit; sequence analysis; structural genes; transcriptomics; unigenes;     Show all 15 Subjects
Abstract:
... Study on kiwifruit (Actinidia chinensis and A. deliciosa) color mainly concentrated in green and yellow-fleshed cultivars, less about molecular mechanism of red-fleshed trait formation, rarely in all red-fleshed fruit. Using ‘Tianyuanhong’ and ‘Yongfengyihao’ (‘TY’, a kind of all red-fleshed cultivar, from Actinidia arguta; ‘YF’, a kind of all green-fleshed cultivar, also from Actinidia arguta) as ...
DOI:
10.1016/j.gene.2018.01.022

27. Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

Author:
Albert, Elise; Duboscq, Renaud; Latreille, Muriel; Santoni, Sylvain; Beukers, Matthieu; Bouchet, Jean‐Paul; Bitton, Fréderique; Gricourt, Justine; Poncet, Charles; Gautier, Véronique; Jiménez‐Gómez, José M.; Rigaill, Guillem; Causse, Mathilde
Source:
Theplant journal 2018 v.96 no.3 pp. 635-650
ISSN:
0960-7412
Subject:
transcriptome,   etc   ; cherries; enzymes; fruits; gene expression; genes; genotype; genotype-environment interaction; hybrids; inbred lines; inheritance (genetics); leaves; loci; messenger RNA; metabolism; phenotype; quantitative trait loci; sugars; tomatoes; transcriptomics;     Show all 20 Subjects
Abstract:
... Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype‐by‐environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome‐wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large ...
DOI:
10.1111/tpj.14057

28. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA

Author:
Molodtsov, Vadim; Sineva, Elena; Zhang, Lu; Huang, Xuhui; Cashel, Michael; Ades, Sarah E.; Murakami, Katsuhiko S.
Source:
Molecular cell 2018 v.69 no.5 pp. 828-839.e5
ISSN:
1097-2765
Subject:
transcriptome,   etc   ; DNA; DNA-directed RNA polymerase; Escherichia coli; active sites; binding sites; crystal structure; models; pleiotropy; ribosomal RNA; ribosomes; stress response; synergism; transcription (genetics);     Show all 14 Subjects
Abstract:
... DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in ...
DOI:
10.1016/j.molcel.2018.01.035

29. Alpha satellite DNA biology: finding function in the recesses of the genome

Author:
McNulty, Shannon M.; Sullivan, Beth A.
Source:
Chromosome research 2018 v.26 no.3 pp. 115-138
ISSN:
0967-3849
Subject:
transcriptome,   etc   ; epigenetics; genome; genome assembly; genomics; high-throughput nucleotide sequencing; humans; intergenic DNA; kinetochores; messenger RNA; non-coding RNA; proteins; satellite DNA; satellite RNA; satellites; transcription (genetics);     Show all 16 Subjects
Abstract:
... Repetitive DNA, formerly referred to by the misnomer “junk DNA,” comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assembli ...
DOI:
10.1007/s10577-018-9582-3

30. Alteration of mammary gland development by bisphenol a and evidence of a mode of action mediated through endocrine disruption

Author:
Perrot-Applanat, Martine; Kolf-Clauw, Martine; Michel, Cécile; Beausoleil, Claire
Source:
Molecular and cellular endocrinology 2018
ISSN:
0303-7207
Subject:
transcriptome,   etc   ; apoptosis; biomechanics; bisphenol A; carcinogens; developmental stages; endocrine-disrupting chemicals; epigenetics; epithelial cells; epithelium; estrogens; extracellular matrix; focal adhesions; humans; immune response; mammary development; mammary glands; mechanism of action; phenotype; signal transduction;     Show all 20 Subjects
Abstract:
... The development and function of the mammary gland are endocrine-dependent processes, depending on the stage of development. Foetal and/or postnatal exposure to low doses of BPA alters tissue organisation through epithelial proliferation and stroma-epithelial interactions. BPA also alters the expression of E2-dependent epithelial and stroma transcriptomes. Several signalling pathways are consistent ...
DOI:
10.1016/j.mce.2018.06.015

31. Alternative polyadenylation is involved in auxin‐based plant growth and development

Author:
Hong, Liwei; Ye, Congting; Lin, Juncheng; Fu, Haihui; Wu, Xiaohui; Li, Qingshun Q.
Source:
The plant journal 2018 v.93 no.2 pp. 246-258
ISSN:
0960-7412
Subject:
transcriptome,   etc   ; 3' untranslated regions; auxins; binding proteins; genes; growth and development; mutants; plant growth;     Show all 8 Subjects
Abstract:
... Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre‐mRNA post‐transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of po ...
DOI:
10.1111/tpj.13771

32. Alternative splicing links histone modifications to stem cell fate decision

Author:
Xu, Yungang; Zhao, Weiling; Olson, Scott D.; Prabhakara, Karthik S.; Zhou, Xiaobo
Source:
Genome biology 2018 v.19 no.1 pp. 133
ISSN:
1474-760X
Subject:
transcriptome,   etc   ; DNA damage; alternative splicing; cell differentiation; data collection; embryonic stem cells; epigenetics; exons; histones; humans; interphase; medicine; transcription factors;     Show all 13 Subjects
Abstract:
... BACKGROUND: Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. However, their intricate interrelations and joint contributions to ESC fate dec ...
DOI:
10.1186/s13059-018-1512-3

33. A massive incorporation of microbial genes into the genome of Tetranychus urticae, a polyphagous arthropod herbivore

Author:
Wybouw, N.; Van Leeuwen, T.; Dermauw, W.
Source:
Insect molecular biology 2018 v.27 no.3 pp. 333-351
ISSN:
0962-1075
Subject:
transcriptome,   etc   ; Bemisia tabaci; Nematoda; Tetranychus urticae; bacteria; beta-alanine; biosynthesis; carbohydrates; genes; herbivores; lipids; mites; pantothenic acid; plants (botany); screening; transferases; vitamin metabolism;     Show all 17 Subjects
Abstract:
... A number of horizontal gene transfers (HGTs) have been identified in the spider mite Tetranychus urticae, a chelicerate herbivore. However, the genome of this mite species has at present not been thoroughly mined for the presence of HGT genes. Here, we performed a systematic screen for HGT genes in the T. urticae genome using the h‐index metric. Our results not only validated previously identified ...
DOI:
10.1111/imb.12374

34. A multilocus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild‐collected Arabidopsis thaliana

Author:
Zan, Yanjun; Carlborg, Örjan
Source:
Molecular ecology resources 2018 v.18 no.4 pp. 798-808
ISSN:
1755-098X
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; alleles; flowering date; gene expression; genetic traits; genomics; genotype; habitats; kinship; loci; models; phenotype; phenotypic variation; screening;     Show all 15 Subjects
Abstract:
... The adaptation to a new habitat often results in a confounding between genomewide genotype and beneficial alleles. When the confounding is strong, or the allelic effects is weak, it is a major statistical challenge to detect the adaptive polymorphisms. We describe a novel approach to dissect polygenic traits in natural populations. First, candidate adaptive loci are identified by screening for loc ...
DOI:
10.1111/1755-0998.12757

35. A Myb transcription factor represses conidiation and cephalosporin C production in Acremonium chrysogenum

Author:
Wang, Ying; Hu, Pengjie; Li, Honghua; Wang, Yanling; Long, Liang-kun; Li, Kuan; Zhang, Xiaoling; Pan, Yuanyuan; Liu, Gang
Source:
Fungal genetics and biology 2018 v.118 pp. 1-9
ISSN:
1087-1845
Subject:
transcriptome,   etc   ; Acremonium chrysogenum; biosynthesis; cephalosporins; conidia; conidiation; developmental stages; gene expression regulation; mutants; open reading frames; polymerase chain reaction; red fluorescent protein; regulator genes; sequence analysis; transcription (genetics); transcription factors; transfer DNA;     Show all 17 Subjects
Abstract:
... Acremonium chrysogenum is the industrial producer of cephalosporin C (CPC). We isolated a mutant (AC554) from a T-DNA inserted mutant library of A. chrysogenum. AC554 exhibited a reduced conidiation and lack of CPC production. In consistent with it, the transcription of cephalosporin biosynthetic genes pcbC and cefEF was significantly decreased in AC554. Thermal asymmetric interlaced polymerase ch ...
DOI:
10.1016/j.fgb.2018.05.006

36. Analyses of the transcriptome of Bombyx mori cells infected with either BmNPV or AcMNPV

Author:
Chen, Yu-Wei; Wu, Carol-P; Wu, Tsai-Chin; Wu, Yueh-Lung
Source:
Journal of Asia-Pacific entomology 2018 v.21 no.1 pp. 37-45
ISSN:
1226-8615
Subject:
transcriptome,   etc   ; Autographa californica; Autographa californica multiple nucleopolyhedrovirus; Bombyx mori; Bombyx mori nucleopolyhedrovirus; RNA interference; genes; high-throughput nucleotide sequencing; host range; host specificity; host-pathogen relationships; hosts; immune response; microRNA; pathogens; protein synthesis; prototypes; silkworms; viruses;     Show all 19 Subjects
Abstract:
... Baculoviruses are insect-specific DNA viruses with a restricted host range. Two examples of such include Autographa californica nucleopolyhedrovirus (AcMNPV) and Bombyx mori nucleopolyhedrovirus (BmNPV). AcMNPV is a commercially available and widely used baculovirus prototype which can infect 39 species in 13 families. On the other hand, BmNPV is a major pathogen of silkworms which has developed h ...
DOI:
10.1016/j.aspen.2017.10.009

37. Analysis of DNA methylome and transcriptome profiling following Gibberellin A3 (GA3) foliar application in Nicotiana tabacum L.

Author:
Manoharlal, Raman; Saiprasad, G. V. S.; Kaikala, Vinay; Suresh Kumar, R.; Kovařík, Ales
Source:
Indian journal of plant physiology 2018 v.23 no.3 pp. 543-556
ISSN:
0019-5502
Subject:
transcriptome,   etc   ; DNA; DNA hypomethylation; Nicotiana tabacum; foliar application; gene expression; gene silencing; genes; gibberellic acid; landscapes; microarray technology; models; transcriptomics;     Show all 13 Subjects
Abstract:
... The present work investigated a comprehensive genome-wide landscape of DNA methylome and its relationship with transcriptome upon gibberellin A₃ (GA₃) foliar application under practical field conditions in solanaceae model, Nicotiana tabacum L. Methylated DNA Immunoprecipitation-Sequencing (MeDIP-Seq) analysis uncovered over 82% (18,456) of differential methylated regions (DMRs) in intergenic-regi ...
DOI:
10.1007/s40502-018-0393-5

38. Analysis of snake venom metalloproteinases from Myanmar Russell's viper transcriptome

Author:
Yee, Khin Than; Tongsima, Sissades; Vasieva, Olga; Ngamphiw, Chumpol; Wilantho, Alisa; Wilkinson, Mark C.; Somparn, Poorichya; Pisitkun, Trairak; Rojnuckarin, Ponlapat
Source:
Toxicon 2018 v.146 pp. 31-41
ISSN:
0041-0101
Subject:
transcriptome,   etc   ; Daboia russelii; Vipera; amino acid sequences; basement membrane; bioactive properties; blood coagulation factors; blood platelets; computer software; endothelial cells; females; genetic databases; habitats; hemostasis; high-throughput nucleotide sequencing; males; mass spectrometry; messenger RNA; metalloproteinases; polyacrylamide gel electrophoresis; snake venoms;     Show all 21 Subjects
Abstract:
... Snake venom metalloproteinases (SVMPs) are the key enzymes in Russell's viper (RV) venom which target all important components of haemostasis, such as clotting factors, platelets, endothelial cells and basement membrane. The structural diversity of SVMPs contributes to the broad spectrum of biological activities. The aim of the study was to investigate the SVMP transcript profile to gain better in ...
DOI:
10.1016/j.toxicon.2018.03.005

39. Analysis of the DNA methylation patterns and transcriptional regulation of the NB-LRR-encoding gene family in Arabidopsis thaliana

Author:
Kong, Weiwen; Li, Bin; Wang, Qianqian; Wang, Bin; Duan, Xiaoke; Ding, Li; Lu, Yanke; Liu, Li-Wei; La, Honggui
Source:
Plant molecular biology 2018 v.96 no.6 pp. 563-575
ISSN:
0167-4412
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; DNA; DNA methylation; disease resistance; eukaryotic cells; gene expression; gene expression regulation; genes; mutants; proteins; reverse transcriptase polymerase chain reaction; transcription (genetics);     Show all 13 Subjects
Abstract:
... KEY MESSAGE: The relationships between transcription and methylation were revealed in Arabidopsis thaliana NB-LRR-encoding genes in wild type (Col-0) and different mutants. Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins constitute a large family that plays predominant roles in disease resistance. However, the regulation of NB-LRR-encoding genes at the transcriptional level is stil ...
DOI:
10.1007/s11103-018-0715-z

40. Analysis of the grapevine moth Lobesia botrana antennal transcriptome and expression of odorant-binding and chemosensory proteins

Author:
Rojas, Valentina; Jiménez, Héctor; Palma-Millanao, Rubén; González-González, Angélica; Machuca, Juan; Godoy, Ricardo; Ceballos, Ricardo; Mutis, Ana; Venthur, Herbert
Source:
Comparative biochemistry and physiology 2018 v.27 pp. 1-12
ISSN:
1744-117X
Subject:
transcriptome,   etc   ; Lobesia botrana; Vitis; antennae; chemoreceptors; control methods; females; high-throughput nucleotide sequencing; males; messenger RNA; monitoring; moths; odorant receptors; pests; phylogeny; population density; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sex pheromones; taste; vineyards; Chile; Europe; North America;     Show all 24 Subjects
Abstract:
... The grapevine moth, Lobesia botrana, is considered a harmful pest for vineyards in Chile as well as in North America and Europe. Currently, monitoring and control methods of L. botrana are based on its main sex pheromone component, being effective for low population densities. In order to improve control methods, antennal olfactory proteins in moths, such as odorant-binding proteins (OBPs) and odo ...
DOI:
10.1016/j.cbd.2018.04.003

41. Analysis of the transcription factors expressed in the mature seed embryos of Moringa oleifera Lam. using RNA-sequencing and de novo transcriptome assembly

Author:
Panes, V. A.; Baoas, R. D.
Source:
Acta horticulturae 2018 no.1205 pp. 705-716
ISSN:
0567-7572
Subject:
transcriptome,   etc   ; Moringa oleifera; Theobroma cacao; antioxidants; bioinformatics; biological control; bioremediation; biosynthesis; databases; energy; environmental factors; gene expression; genes; nutrition; oils; quantitative polymerase chain reaction; sequence analysis; stress response; therapeutics; transcription (genetics); transcription factors;     Show all 21 Subjects
Abstract:
... Moringa oleifera Lam. is well known for its numerous documented properties, particularly its significant applications in nutrition, therapeutics, biocontrol, energy, and bioremediation. These properties are the consequences of the vibrant physiological processes of the plant in the context of the ever-changing biotic and abiotic factors, in which transcription factors play substantial roles. Trans ...
DOI:
10.17660/ActaHortic.2018.1205.87

42. Analysis of three types of resistance gene analogs in PmU region from Triticum urartu

Author:
ZHANG, Lei; ZHENG, Xing-wei; QIAO, Lin-yi; QIAO, Ling; ZHAO, Jia-jia; WANG, Jian-ming; ZHENG, Jun
Source:
Journal of integrative agriculture 2018 v.17 no.12 pp. 2601-2611
ISSN:
2095-3119
Subject:
transcriptome,   etc   ; Blumeria graminis f. sp. tritici; Triticum urartu; binding sites; breeding; chromosomes; cluster analysis; databases; disease resistance; genetic markers; genomics; protein kinases; quantitative polymerase chain reaction; resistance genes; reverse transcriptase polymerase chain reaction; screening; wheat;     Show all 17 Subjects
Abstract:
... Resistance gene analog (RGA) screening of mapped disease-resistant genes not only helps to clone these genes but also helps to develop efficient molecular markers for resistance breeding. The present study focused on the PmU region located on chromosome 7AuL of Triticum urartu, and recently, a nucleotide binding site (NBS)-encoding gene, Pm60, was cloned from the same chromosome arm. In this resea ...
DOI:
10.1016/S2095-3119(18)61995-1

43. Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

Author:
Chao, Yuehui; Yuan, Jianbo; Li, Sifeng; Jia, Siqiao; Han, Liebao; Xu, Lixin
Source:
BMC plant biology 2018 v.18 no.1 pp. 300
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Trifolium pratense; alfalfa; alternative splicing; cold season; forage legumes; introns; messenger RNA; non-coding RNA;     Show all 9 Subjects
Abstract:
... BACKGROUND: Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover. RESULTS: In this study, the red clover transcriptome was sequenced using sin ...
DOI:
10.1186/s12870-018-1534-8

44. Analyzing trichomes and spatio-temporal expression of a cysteine protease gene Mucunain in Mucuna pruriens L. (DC)

Author:
Singh, SusheelKumar; Dhawan, SunitaSingh
Source:
Protoplasma 2018 v.255 no.2 pp. 575-584
ISSN:
0033-183X
Subject:
transcriptome,   etc   ; Mucuna pruriens; Parkinson disease; cysteine proteinases; cytoplasm; flowers; genotype; leaves; legumes; medicinal plants; mutants; pruritus; seeds; trichomes; unigenes;     Show all 15 Subjects
Abstract:
... Mucuna pruriens is a well-known legume for the itching attributes of the trichome and a valuable medicinal herb that is used for the treatment of Parkinson’s disease, sexual debilities, etc. Its cultivation was deprived due to its itching behavior. The wild genotype of M. pruriens have the largest trichome length (2015 ± 29 μm) compared to other genotype and mutants. The white-seeded variety of M. ...
DOI:
10.1007/s00709-017-1164-2

45. An annotated transcriptome of highly inbred Thuja plicata (Cupressaceae) and its utility for gene discovery of terpenoid biosynthesis and conifer defense

Author:
Shalev, TalJ.; Yuen, MacaireM. S.; Gesell, Andreas; Yuen, Agnes; Russell, JohnH.; Bohlmann, Jörg
Source:
Tree genetics & genomes 2018 v.14 no.3 pp. 35
ISSN:
1614-2942
Subject:
transcriptome,   etc   ; Pinaceae; Thuja plicata; biosynthesis; breeding; browsing; conifers; forests; genes; genomics; herbivores; heterozygosity; leaves; monoterpenoids; phylogeny; seedlings; statistical analysis; transcriptomics; trees; ungulates;     Show all 20 Subjects
Abstract:
... Western redcedar (Thuja plicata; Cupressaceae; WRC) is an ecologically and economically important conifer species of the Pacific Northwest. Regeneration of WRC forests is affected by ungulate browsing, which removes current growth and hampers development of young trees. Monoterpenes make WRC foliage less palatable and can deter browsing. Genomic resources are required to advance knowledge of terpe ...
DOI:
10.1007/s11295-018-1248-y

46. Ancestral transcriptome inference based on RNA-Seq and ChIP-seq data

Author:
Yang, Jingwen; Ruan, Hang; Zou, Yangyun; Su, Zhixi; Gu, Xun
Source:
Methods 2018
ISSN:
1046-2023
Subject:
transcriptome,   etc   ; Animalia; case studies; chromatin; computer software; high-throughput nucleotide sequencing; liver; metabolomics; methylation; mice; models; phylogeny; proteomics; transcription (genetics); transcription factors;     Show all 15 Subjects
Abstract:
... With the help of high-throughput NGS (next-generation sequencing) technologies, ancestral transcriptome reconstruction is helpful to understand the complexity of transcriptional regulatory systems that underlies the evolution of multiple cellular metazoans with sophisticated functions and distinctive morphologies. To this end, we report a new method of ancestral state inference. The new method use ...
DOI:
10.1016/j.ymeth.2018.11.010

47. An efficient method for developing polymorphic microsatellite markers from high-throughput transcriptome sequencing: a case study of hexaploid oil-tea camellia (Camellia oleifera)

Author:
Cui, Xiangyan; Huang, Xiaomao; Chen, Jiaming; Yang, Xiaoqiang; Rong, Jun
Source:
Euphytica 2018 v.214 no.2 pp. 26
ISSN:
0014-2336
Subject:
transcriptome,   etc   ; Camellia oleifera; alleles; altitude; case studies; genetic markers; genetic variation; hexaploidy; high-throughput nucleotide sequencing; leaves; microsatellite repeats; mountains; plant breeding; screening; transcriptomics; China;     Show all 16 Subjects
Abstract:
... The bottleneck of microsatellite marker development is to determine polymorphisms of microsatellite markers. A large amount of microsatellites can be detected via high-throughput sequencing. However, most previous studies didn’t fully use the high-throughput sequencing data to predict number of alleles at microsatellite loci. Instead, laborious experiments were performed for manually screening mic ...
DOI:
10.1007/s10681-018-2114-6

48. A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production

Author:
Geisler, Christoph
Source:
BMC biotechnology 2018 v.18 no.1 pp. 8
ISSN:
1472-6750
Subject:
transcriptome,   etc   ; Errantivirus; Spodoptera frugiperda; bioinformatics; biosafety; cell lines; genetic databases; genome; high-throughput nucleotide sequencing; insect viruses; insects; open reading frames; proteins; transposons; viruses;     Show all 15 Subjects
Abstract:
... BACKGROUND: Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although ...
DOI:
10.1186/s12896-017-0412-z
PubMed:
29415704
PubMed Central:
PMC5803895

49. A new mechanistic understanding of light-limitation in the seagrass Zostera muelleri

Author:
Davey, Peter A.; Pernice, Mathieu; Ashworth, Justin; Kuzhiumparambil, Unnikrishnan; Szabó, Milán; Dolferus, Rudy; Ralph, Peter J.
Source:
Marine environmental research 2018 v.134 pp. 55-67
ISSN:
0141-1136
Subject:
transcriptome,   etc   ; Zostera; abscisic acid; chlorophyll; fluorometry; gene expression regulation; genes; genetic markers; high performance liquid chromatography; monitoring; photons; photosystem II; seagrasses;     Show all 13 Subjects
Abstract:
... In this study we investigated the effect of light-limitation (∼20 μmol photons m−2 s−1) on the southern hemisphere seagrass, Zostera muelleri. RNA sequencing, chlorophyll fluorometry and HPLC techniques were used to investigate how the leaf-specific transcriptome drives changes in photosynthesis and photo-pigments in Z. muelleri over 6 days. 1593 (7.51%) genes were differentially expressed on day ...
DOI:
10.1016/j.marenvres.2017.12.012

50. A new water soluble copper N-heterocyclic carbene complex delivers mild O⁶G-selective RNA alkylation

Author:
Rasale, Dnyaneshwar; Patil, Kiran; Sauter, Basilius; Geigle, Stefanie; Zhanybekova, Saule; Gillingham, Dennis
Source:
Chemical communications 2018 v.54 no.66 pp. 9174-9177
ISSN:
1364-548X
Subject:
transcriptome,   etc   ; DNA; acetamides; alkylation; carbenes; copper; diazo compounds; guanine; messenger RNA; mutagens; water solubility;     Show all 11 Subjects
Abstract:
... We show here that copper carbenes generated from diazo acetamides alkylate single RNAs, mRNAs, or pools of total transcriptome RNA, delivering exclusively alkylation at the O⁶ position in guanine (O⁶G). Although the reaction is effective with free copper some RNA fragmentation occurs, a problem we resolve by developing a novel water-stable copper N-heterocyclic carbene complex. Carboxymethyl adduc ...
DOI:
10.1039/c8cc04476g