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Plant genomics

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https://www.readbyqxmd.com/read/28453813/identification-and-allelic-dissection-uncover-roles-of-lncrnas-in-secondary-growth-of-populus-tomentosa
#1
Daling Zhou, Qingzhang Du, Jinhui Chen, Qingshi Wang, Deqiang Zhang
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation...
April 26, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28453782/sempi-a-genome-based-secondary-metabolite-prediction-and-identification-web-server
#2
Paul F Zierep, Natàlia Padilla, Dimitar G Yonchev, Kiran K Telukunta, Dennis Klementz, Stefan Günther
The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453685/phenocurve-capturing-dynamic-phenotype-environment-relationships-using-phenomics-data
#3
Yifan Yang, Lei Xu, Zheyun Feng, Jeffrey A Cruz, Linda J Savage, David M Kramer, Jin Chen
Motivation: Phenomics is essential for understanding the mechanisms that regulate or influence growth, fitness, and development. Techniques have been developed to conduct high-throughput large-scale phenotyping on animals, plants and humans, aiming to bridge the gap between genomics, gene functions and traits. Although new developments in phenotyping techniques are exciting, we are limited by the tools to analyze fully the massive phenotype data, especially the dynamic relationships between phenotypes and environments...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453650/plantismash-automated-identification-annotation-and-expression-analysis-of-plant-biosynthetic-gene-clusters
#4
Satria A Kautsar, Hernando G Suarez Duran, Kai Blin, Anne Osbourn, Marnix H Medema
Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448743/circular-rnas-with-hammerhead-ribozymes-encoded-in-eukaryotic-genomes-the-enemy-at-home
#5
Marcos de la Peña, Amelia Cervera
A new family of non-autonomous retrotransposons with self-cleaving hammerhead ribozymes, the so called retrozymes, has recently been found encoded in a number of plant genomes. These retroelements can be actively transcribed, and their RNAs accumulate in the cells as abundant non-coding circular RNAs (circRNAs) of small size (600-1000 nt). Related circRNAs with self-cleaving ribozymes had already been described in plants, and belong to a group of infectious RNA agents with an uncertain origin: the viroids and viroid-like satellites of plant RNA viruses...
April 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28448529/a-genome-wide-analysis-of-the-rna-guided-silencing-pathway-in-coffee-reveals-insights-into-its-regulatory-mechanisms
#6
Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antonio Chalfun-Junior
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover...
2017: PloS One
https://www.readbyqxmd.com/read/28448006/purification-of-high-molecular-weight-genomic-dna-from-powdery-mildew-for-long-read-sequencing
#7
Joanna M Feehan, Katherine E Scheibel, Salim Bourras, William Underwood, Beat Keller, Shauna C Somerville
The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum...
March 31, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447887/cyclopiazonic-acid-is-a-pathogenicity-factor-for-aspergillus-flavus-and-a-promising-target-for-screening-germplasm-for-ear-rot-resistance
#8
Subbaiah C Chalivendra, Catherine DeRobertis, Perng-Kuang Chang, Kenneth E Damann
Aspergillus flavus, an opportunistic pathogen, contaminates maize and other key crops with carcinogenic aflatoxins (AFs). Besides AFs, A. flavus makes many more secondary metabolites (SMs) whose toxicity in insects or vertebrates has been studied. However, the role of SMs in the invasion of plant hosts by A. flavus remains to be investigated. Cyclopiazonic acid (CPA), a neurotoxic SM made by A. flavus, is a nanomolar inhibitor of endoplasmic reticulum calcium ATPases (ECAs) and a potent inducer of cell death in plants...
April 24, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28447630/plant-science-genomic-compartments-in-barley
#9
Beat Keller, Simon G Krattinger
No abstract text is available yet for this article.
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28447607/genome-wide-identification-characterization-and-expression-profile-of-aquaporin-gene-family-in-flax-linum-usitatissimum
#10
S M Shivaraj, Rupesh K Deshmukh, Rhitu Rai, Richard Bélanger, Pawan K Agrawal, Prasanta K Dash
Membrane intrinsic proteins (MIPs) form transmembrane channels and facilitate transport of myriad substrates across the cell membrane in many organisms. Majority of plant MIPs have water transporting ability and are commonly referred as aquaporins (AQPs). In the present study, we identified aquaporin coding genes in flax by genome-wide analysis, their structure, function and expression pattern by pan-genome exploration. Cross-genera phylogenetic analysis with known aquaporins from rice, arabidopsis, and poplar showed five subgroups of flax aquaporins representing 16 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), 2 small basic intrinsic proteins (SIPs), and 3 uncharacterized intrinsic proteins (XIPs)...
April 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28447400/genome-wide-identification-of-pathogenicity-conidiation-and-colony-sectorization-genes-in-metarhizium-robertsii
#11
Guohong Zeng, Xiaoxuan Chen, Xing Zhang, Qiangqiang Zhang, Chuan Xu, Wubin Mi, Na Guo, Hong Zhao, Yue You, Farah-Jade Dryburgh, Michael J Bidochka, Raymond J St Leger, Lei Zhang, Weiguo Fang
Metarhizium robertsii occupies a wide array of ecological niches and has diverse lifestyle options (saprophyte, insect pathogen and plant symbiont), that renders it an unusually effective model for studying genetic mechanisms for fungal adaptation. Here we screened over 20,000 M. robertsii T-DNA mutants in order to elucidate genetic mechanism by which M. robertsii replicates and persists in diverse niches. We identified 287 conidiation, colony sectorization or pathogenicity loci, many of which have not been reported in other fungi...
April 26, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28446920/two-highly-similar-poplar-paleo-subgenomes-suggest-an-autotetraploid-ancestor-of-salicaceae-plants
#12
Yinzhe Liu, Jinpeng Wang, Weina Ge, Zhenyi Wang, Yuxian Li, Nanshan Yang, Sangrong Sun, Liwei Zhang, Xiyin Wang
As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446764/complexity-of-genetic-mechanisms-conferring-nonuniformity-of-recombination-in-maize
#13
Qingchun Pan, Min Deng, Jianbing Yan, Lin Li
Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446635/a-motif-and-amino-acid-bias-bioinformatics-pipeline-to-identify-hydroxyproline-rich-glycoproteins
#14
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signalling and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive post-translational modifications (glycosylation) and have been implicated in many biological functions...
April 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28446145/genome-wide-analysis-of-atp-binding-cassette-abc-transporters-in-the-sweetpotato-whitefly-bemisia-tabaci
#15
Lixia Tian, Tianxue Song, Rongjun He, Yang Zeng, Wen Xie, Qingjun Wu, Shaoli Wang, Xuguo Zhou, Youjun Zhang
BACKGROUND: ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, we annotated ABC transporters from a newly sequenced sweetpotato whitefly genome. Bemisia tabaci Q biotype is an emerging global invasive species that has caused extensive damages to field crops as well as ornamental plants. RESULTS: A total of 55 ABC transporters containing all eight described subfamilies (A to H) were identified in the B...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28445834/light-harvesting-antenna-complexes-in-the-moss-physcomitrella-patens-implications-for-the-evolutionary-transition-from-green-algae-to-land-plants
#16
REVIEW
Masakazu Iwai, Makio Yokono
Plants have successfully adapted to a vast range of terrestrial environments during their evolution. To elucidate the evolutionary transition of light-harvesting antenna proteins from green algae to land plants, the moss Physcomitrella patens is ideally placed basally among land plants. Compared to the genomes of green algae and land plants, the P. patens genome codes for more diverse and redundant light-harvesting antenna proteins. It also encodes Lhcb9, which has characteristics not found in other light-harvesting antenna proteins...
April 23, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28445833/phytochrome-diversification-in-cyanobacteria-and-eukaryotic-algae
#17
REVIEW
Nathan C Rockwell, J Clark Lagarias
Phytochromes control almost every aspect of plant biology, including germination, growth, development, and flowering, in response to red and far-red light. These photoreceptors thus hold considerable promise for engineering crop plant responses to light. Recently, structural research has shed new light on how phytochromes work. Genomic and transcriptomic studies have improved our understanding of phytochrome loss, retention, and diversification during evolution. We are also beginning to understand phytochrome function in cyanobacteria and eukaryotic algae...
April 22, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28444595/cloning-and-characterization-of-auxin-efflux-carrier-genes-ecpin1a-and-ecpin1b-from-finger-millet-eleusine-coracana-l
#18
Tapan Kumar Mohanta, Hanhong Bae
Auxin signaling events in plants play important role in developmental regulation as well as gravitropic responses and plays crucial role in the development of root, lateral root and root hairs. The gene that is known to be most important in the development of root, lateral root and root hairs is commonly known as auxin efflux carrier (PIN). Being commonly known as orphan plant, the genome sequence of Eleusine coracana is not known yet, and hence it was very difficult to conduct advanced research in root development in this plant...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444590/transcripts-of-pectin-degrading-enzymes-and-isolation-of-complete-cdna-sequence-of-a-pectate-lyase-gene-induced-by-coffee-white-stem-borer-xylotrechus-quadripes-in-the-bark-tissue-of-coffea-canephora-robusta-coffee
#19
Kosaraju Bharathi, P Santosh, H L Sreenath
Of the two commercially cultivated coffee (Coffea) species, C. arabica (arabica) is highly susceptible and C. canephora (robusta) is highly resistant to the insect pest Xylotrechus quadripes (Coleoptera: Cerambycidae), commonly known as coffee white stem borer (CWSB). We constructed a forward-subtracted cDNA library by Suppression Subtractive Hybridization (SSH) from robusta bark tissue for profiling genes induced by CWSB infestation. Among the 265 unigenes of the SSH EST library, 7 unigenes (5 contigs and 2 singletons) matching different pectin-degrading enzymes were discovered...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444368/simultaneous-targeting-of-multiple-gene-homeologues-to-alter-seed-oil-production-in-camelina-sativa
#20
J A Aznar-Moreno, T P Durrett
The ability to easily transform Camelina sativa with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologues can encode for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways...
April 21, 2017: Plant & Cell Physiology
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