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https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#1
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28225035/deep-sequencing-and-transcriptome-analyses-to-identify-genes-involved-in-secoiridoid-biosynthesis-in-the-tibetan-medicinal-plant-swertia-mussotii
#2
Yue Liu, Yi Wang, Fengxian Guo, Lin Zhan, Toni Mohr, Prisca Cheng, Naxin Huo, Ronghui Gu, Danning Pei, Jiaqing Sun, Li Tang, Chunlin Long, Luqi Huang, Yong Q Gu
Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties effective in the treatment of various ailments including hepatitis. Secoiridoids are the major bioactive compounds in S. mussotii. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from the root, leaf, stem, and flower tissues, and performed de novo sequence assembly, yielding 98,613 unique transcripts with an N50 of 1,085 bp. Putative functions could be assigned to 35,029 transcripts (35...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223998/rna-seq-analysis-of-cold-and-drought-responsive-transcriptomes-of-zea-mays-ssp-mexicana-l
#3
Xiang Lu, Xuan Zhou, Yu Cao, Meixue Zhou, David McNeil, Shan Liang, Chengwei Yang
The annual Zea mays ssp. mexicana L. is a member of teosinte, a wild relative of the Zea mays spp. mays L. This subspecies has strong growth and regeneration ability, high tiller numbers, high protein and lysine content as well as resistance to many fungal diseases, and it can be effectively used in maize improvement. In this study, we reported a Zea mays ssp. mexicana L. transcriptome by merging data from untreated control (CK), cold (4°C) and drought (PEG2000, 20%) treated plant samples. A total of 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp) were predicted, which code for homologs of near 47% of the published maize proteome...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223989/ufgt-the-key-enzyme-associated-with-the-petals-variegation-in-japanese-apricot
#4
Xinxin Wu, Qinghua Gong, Xiaopeng Ni, Yong Zhou, Zhihong Gao
Japanese apricot (Prunus mume Sieb.et Zucc.) is an important ornamental plant in China. One of the traits of petals color variegation is attractive, but its formation mechanism is unclear. In our study, RNA-seq technology was employed to characterize the transcriptome response to the mutation of "Fuban Tiaozhi" associated with petals variegation in Japanese apricot. As a result, 4,579,040 (white-flowered, WF) and 7,269,883 (red-flowered, RF) reads were mapped to P. persica genes, while 5,006,676 (WF) and 7,907,436 (RF) were mapped to P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223714/comparative-physiological-and-transcriptomic-analyses-provide-integrated-insight-into-osmotic-cold-and-salt-stress-tolerance-mechanisms-in-banana
#5
Wei Hu, Zehong Ding, Weiwei Tie, Yan Yan, Yang Liu, Chunlai Wu, Juhua Liu, Jiashui Wang, Ming Peng, Biyu Xu, Zhiqiang Jin
The growth, development, and production of banana plants are constrained by multiple abiotic stressors. However, it remains elusive for the tolerance mechanisms of banana responding to multiple abiotic stresses. In this study, we found that Fen Jiao (FJ) was more tolerant to osmotic, cold, and salt stresses than BaXi Jiao (BX) by phenotypic and physiological analyses. Comparative transcriptomic analyses highlighted stress tolerance genes that either specifically regulated in FJ or changed more than twofold in FJ relative to BX after treatments...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223441/rima-dependent-nuclear-accumulation-of-iyo-triggers-auxin-irreversible-cell-differentiation-in-arabidopsis
#6
Alfonso Muñoz, Silvina Mangano, Mary Paz González-García, Ramón Contreras, Michael B Sauer, Bert De Rybel, Dolf Weijers, José J Sánchez-Serrano, Maite Sanmartín, Enrique Rojo
The transcriptional regulator MINIYO (IYO) is essential and rate-limiting for initiating cell differentiation in Arabidopsis thaliana. Moreover, IYO moves from the cytosol into the nucleus in cells at the meristem periphery, possibly triggering their differentiation. However, the genetic mechanisms controlling IYO nuclear accumulation were unknown and the evidence that increased nuclear IYO levels trigger differentiation remained correlative. Searching for IYO interactors, we have identified RPAP2 IYO Mate (RIMA), a homologue of yeast and human proteins linked to nuclear import of selective cargo...
February 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28222234/transcriptome-analysis-of-the-brassica-napus-leptosphaeria-maculans-pathosystem-identifies-receptor-signalling-and-structural-genes-underlying-plant-resistance
#7
Michael G Becker, Xuehua Zhang, Philip L Walker, Joey C Wan, Jenna L Millar, Deirdre Khan, Matthew J Granger, Jacob D Cavers, Ainsley C Chan, Dilantha W G Fernando, Mark F Belmonte
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant yield loss worldwide. While genetic resistance has been used to mitigate the disease using traditional breeding strategies, there is little knowledge about the genes contributing to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L...
February 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28222171/metabolite-profiling-of-the-carnivorous-pitcher-plants-darlingtonia-and-sarracenia
#8
Hannu Hotti, Peddinti Gopalacharyulu, Tuulikki Seppänen-Laakso, Heiko Rischer
Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals...
2017: PloS One
https://www.readbyqxmd.com/read/28222153/dissecting-nutrient-related-co-expression-networks-in-phosphate-starved-poplars
#9
Mareike Kavka, Andrea Polle
Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation...
2017: PloS One
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#10
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28220595/guanosine-tetraphosphate-modulates-salicylic-acid-signaling-and-the-resistance-of-arabidopsis-thaliana-to-turnip-mosaic-virus
#11
Hela Abdelkefi, Matteo Sugliani, Ke Hang, Seddik Harchouni, Ludivine Soubigou-Taconnat, Sylvie Citerne, Gregory Mouille, Hatem Fakhfakh, Christophe Robaglia, Ben Field
Chloroplasts can act as key players in the perception and acclimation of plants to incoming environmental signals. A growing body of evidence indicates that chloroplasts play a critical role in plant immunity. Chloroplast function can be regulated by the nucleotides guanosine tetraphosphate and pentaphosphate ((p)ppGpp). In plants (p)ppGpp levels increase in response to abiotic stress and to plant hormones that are involved in abiotic and biotic stress signaling. Here we analyzed the transcriptome of Arabidopsis plants that over accumulate (p)ppGpp and unexpectedly found a decrease in the levels of a broad range of transcripts for plant defense and immunity...
February 21, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28220591/transcriptome-analysis-of-root-knot-nematode-meloidogyne-incognita-infected-tomato-solanum-lycopersicum-roots-reveals-complex-gene-expression-profiles-and-metabolic-networks-of-both-host-and-nematode-during-susceptible-and-resistance-responses
#12
Neha Shukla, Rachita Yadav, Pritam Kaur, Simon Rasmussen, Shailendra Goel, Manu Agarwal, Arun Jagannath, Ramneek Gupta, Amar Kumar
Root knot nematodes (RKNs, Meloidogyne incognita) are economically important endoparasites having a wide-host range. We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time intervals from susceptible plants and two infection time intervals from resistant plants, grown under soil conditions. Differentially expressed genes during susceptible (1827-tomato, 462-RKN) and resistance (25-tomato, 160-RKN) interactions were identified...
February 21, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28220324/virus-surveys-of-capsicum-spp-in-the-republic-of-benin-reveal-the-prevalence-of-pepper-vein-yellows-virus-and-the-identification-of-a-previously-uncharacterised-polerovirus-species
#13
Leonard Afouda, Daouda Kone, Valerien Zinsou, Laurence Dossou, Lawrence Kenyon, Stephan Winter, Dennis Knierim
Surveys were conducted in 2014 and 2015 in Southern and Northern Benin, respectively, to identify the viruses infecting peppers (Capsicum spp.). The samples were screened by ELISA for cucumber mosaic virus (CMV), pepper veinal mottle virus (PVMV), potato virus Y (PVY) and tomato yellow leaf curl virus (TYLCV). A generic reverse transcription PCR (RT-PCR) was used to test for the presence of poleroviruses. ELISA tests confirmed the prevalence of all viruses, while the RT-PCR detected pepper vein yellows virus (PeVYV) which is reported for the first time in Benin...
February 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28220138/de-novo-transcriptome-assembly-of-phomopsis-liquidambari-provides-insights-into-genes-associated-with-different-lifestyles-in-rice-oryza-sativa-l
#14
Jun Zhou, Xin Li, Yan Chen, Chuan-Chao Dai
The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220135/differential-gene-expression-analysis-in-polygonum-minus-leaf-upon-24-h-of-methyl-jasmonate-elicitation
#15
Reyhaneh Rahnamaie-Tajadod, Kok-Keong Loke, Hoe-Han Goh, Normah M Noor
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219335/stress-responsive-pathways-and-small-rna-changes-distinguish-variable-developmental-phenotypes-caused-by-msh1-loss
#16
Mon-Ray Shao, Sunil Kumar Kenchanmane Raju, John D Laurie, Robersy Sanchez, Sally A Mackenzie
BACKGROUND: Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge...
February 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28218974/molecular-cloning-bioinformatics-analysis-and-transcriptional-profiling-of-jaz1-and-jaz2-from-salvia-miltiorrhiza
#17
Yangyun Zhou, Xun Zhou, Qing Li, Junfeng Chen, Ying Xiao, Lei Zhang, Wansheng Chen
Production of major effective metabolites, tanshinones and lithospermic acid B (LAB), was dramatically enhanced by exogenous jasmonate (JA) treatment in Salvia miltiorrhiza. However, the molecular mechanism of such metabolic activation in S. miltiorrhiza has not been elucidated yet. Here, we focused on jasmonate ZIM-domain (JAZ) proteins that act as repressors of JA signaling. Open reading frames of two novel genes, SmJAZ1 and SmJAZ2, from S. miltiorrhiza were amplified according to the annotation of S. miltiorrhiza transcriptome...
January 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28215140/position-based-nucleotide-analysis-of-mir168-family-in-higher-plants-and-its-targets-in-mammalian-transcripts
#18
Mohammed Javed, Manish Solanki, Anshika Sinha, Lata Israni Shukla
The conserved miR168 family is evaluated for position based nucleotide preference in higher plants. The mature miRNA sequences include miR168-5p and miR168-3p, were obtained from miRBase (v21, June 2014) for 15 families (28 plants) containing a-c subfamilies. The preferred position based nucleotide sequences were obtained for miR168-5p and miR168-3p using Data Analysis in Molecular Biology and Evolution (DAMBE). miR168-5p shows same nucleotides at positions 1-6, 8-9, 11-12, 15-17 and 19. Also, miR168-3p is present in 3 families (10 plants) shows the same nucleotide at position 1-11, 13-15 and 17-21...
February 15, 2017: MicroRNA
https://www.readbyqxmd.com/read/28214372/canonical-and-cellular-pathways-timing-gamete-release-in-acropora-digitifera-okinawa-japan
#19
Y Rosenberg, T Doniger, S Harii, F Sinniger, O Levy
Natural light cycles are important for synchronizing behavioral and physiological rhythms over varying time-periods in both plants and animals. An endogenous clock, regulated by positive and negative elements, interacting in feedback loops, control these rhythms. Many corals exhibit diel cycles of polyp expansion and contraction entrained by solar light patterns and monthly cycles of spawning or planulation that correspond to nocturnal lunar light cycles. However, despite considerable interest in studies of coral reproduction, there is currently not enough molecular information about the cellular pathways involved with synchronizing spawning/planulation in broadcast spawners and brooders...
February 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#20
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
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