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Current Opinion in Plant Biology

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https://www.readbyqxmd.com/read/28343122/genetic-and-epigenetic-variation-of-transposable-elements-in-arabidopsis
#1
REVIEW
Charles J Underwood, Ian R Henderson, Robert A Martienssen
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation...
March 23, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28327435/network-approaches-for-plant-phylogenomic-synteny-analysis
#2
REVIEW
Tao Zhao, M Eric Schranz
Network analysis approaches have been widely applied across disciplines. In biology, network analysis is now frequently adopted to organize protein-protein interactions, organize pathways and/or to interpret gene co-expression patterns. However, comparative genomic analyses still largely rely on pairwise comparisons and linear visualizations between genomes. In this article, we discuss the challenges and prospects for establishing a generalized plant phylogenomic synteny network approach needed to interpret the wealth of new and emerging genomic data...
March 16, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28285128/using-mustard-genomes-to-explore-the-genetic-basis-of-evolutionary-change
#3
REVIEW
Lachezar A Nikolov, Miltos Tsiantis
Recent advances in sequencing technologies and gene manipulation tools have driven mustard species into the spotlight of comparative research and have offered powerful insight how phenotypic space is explored during evolution. Evidence emerged for genome-wide signal of transcription factors and gene duplication contributing to trait divergence, e.g., PLETHORA5/7 in leaf complexity. Trait divergence is often manifested in differential expression due to cis-regulatory divergence, as in KNOX genes and REDUCED COMPLEXITY, and can be coupled with protein divergence...
March 8, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28273484/transposon-mediated-epigenetic-regulation-contributes-to-phenotypic-diversity-and-environmental-adaptation-in-rice
#4
REVIEW
Xianwei Song, Xiaofeng Cao
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity...
March 5, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28258985/gene-body-dna-methylation-in-plants
#5
REVIEW
Adam J Bewick, Robert J Schmitz
The type, amount, and location of DNA methylation within a gene provides pivotal information on the enzymatic pathway by which it was achieved and its functional consequences. In plants (angiosperms specifically), gene body methylation (gbM) refers to genes with an enrichment of CG DNA methylation within the transcribed regions and depletion at the transcriptional start and termination sites. GbM genes often compose the bulk of methylated genes within angiosperm genomes and are enriched for housekeeping functions...
March 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28258986/meiotic-recombination-gets-stressed-out-co-frequency-is-plastic-under-pressure
#6
REVIEW
Jennifer L Modliszewski, Gregory P Copenhaver
Meiotic recombination ensures the fertility of gametes and creates novel genetic combinations. Although meiotic crossover (CO) frequency is under homeostatic control, CO frequency is also plastic in nature and can respond to environmental conditions. Most investigations have focused on temperature and recombination, but other external and internal stimuli also have important roles in modulating CO frequency. Even less is understood about the molecular mechanisms that underly these phenomenon, but recent work has begun to advance our knowledge in this field...
February 27, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28242535/the-genomic-basis-of-adaptation-in-plants
#7
REVIEW
Pádraic J Flood, Angela M Hancock
Plants are powerful models for the study of adaptive evolution. Since they are rooted in place, they must directly face environmental insults, making adaptation to local conditions vital. In addition to adaptation to natural conditions, some plant species have held a central role in human subsistence over the past several thousand years. In these species, humans exerted strong selective pressures on traits of agricultural importance. Recently, an increasing number of studies have aimed to identify the genomic basis of adaptation...
February 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28242534/genome-sequencing-supports-a-multi-vertex-model-for-brassiceae-species
#8
REVIEW
Feng Cheng, Jianli Liang, Chengcheng Cai, Xu Cai, Jian Wu, Xiaowu Wang
The economically important Brassica genus is a good system for studying the evolution of polyploids. Brassica genomes have undergone whole genome triplication (WGT). Subgenome dominance phenomena such as biased gene fractionation and dominant gene expression were observed in tripled genomes of Brassica. The genome of radish (Raphanus sativus), another important crop of tribe Brassiceae, was derived from the same WGT event and shows similar subgenome dominance. These findings and molecular dating indicate that radish occupies a similar evolutionary origin as that of Brassica species...
February 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28235716/genomic-dissection-of-host-microbe-and-microbe-microbe-interactions-for-advanced-plant-breeding
#9
REVIEW
Samuel Kroll, Matthew T Agler, Eric Kemen
Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host...
February 21, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28231512/the-impact-of-third-generation-genomic-technologies-on-plant-genome-assembly
#10
REVIEW
Wen-Biao Jiao, Korbinian Schneeberger
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies...
February 20, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#11
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28226268/recent-progress-in-diatom-genomics-and-epigenomics
#12
REVIEW
Leila Tirichine, Achal Rastogi, Chris Bowler
Diatoms are one of the most diverse and successful groups of phytoplankton at the base of the food chain, sustaining life in the ocean and performing vital biogeochemical functions. The last fifteen years have witnessed the comprehensive analysis of several diatom genomes, revealing that they bear traces of their endosymbiotic origins from algal and heterotrophic ancestors, as well as significant gene transfer from bacteria. Their chimeric genomes are further regulated by a range of chromatin-based processes that are characteristic of both plant and animal genomes...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28182971/wheat-paleohistory-created-asymmetrical-genomic-evolution
#13
REVIEW
Caroline Pont, Jérôme Salse
Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes...
February 6, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28162929/editorial-overview-growth-and-development-change-is-in-the-air-how-plants-modulate-development-in-response-to-the-environment
#14
EDITORIAL
Ji Hoon Ahn, Markus Schmid
No abstract text is available yet for this article.
February 2, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28160617/reinforcing-plant-evolutionary-genomics-using-ancient-dna
#15
REVIEW
Rafal M Gutaker, Hernán A Burbano
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place...
February 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28088028/role-of-small-rnas-in-epigenetic-reprogramming-during-plant-sexual-reproduction
#16
REVIEW
German Martinez, Claudia Köhler
Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability...
January 11, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28063383/push-pull-strategy-in-the-regulation-of-postembryonic-root-development
#17
REVIEW
Goh Choe, Ji-Young Lee
Unlike animals, plants continue to grow throughout their lives. The stem cell niche, protected in meristems of shoots and roots, enables this process. In the root, stem cells produce precursors for highly organized cell types via asymmetric cell divisions. These precursors, which are "transit-amplifying cells," actively divide for several rounds before entering into differentiation programs. In this review, we highlight positive feedback regulation between shoot- and root-ward signals during the postembryonic root growth, which is reminiscent of a "push-pull strategy" in business parlance...
January 4, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27918940/beyond-flexibility-controlling-stem-cells-in-an-ever-changing-environment
#18
REVIEW
Anne Pfeiffer, Christian Wenzl, Jan U Lohmann
Developmental plasticity is a defining feature of plants allowing them to colonize a wide range of different ecosystems by promoting environmental adaptation. Their postembryonic development requires life-long maintenance of stem cells, which are embedded into specialized tissues, called meristems. The shoot apical meristem gives rise to all above ground tissues and is a complex and dynamic three-dimensional structure harboring cells of different clonal origins and fates. Functionally divergent subdomains are stably maintained despite permanent cell division, however their relative sizes are modified in response to developmental and environmental signals...
February 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27886593/the-evolution-of-micrornas-in-plants
#19
REVIEW
Jie Cui, Chenjiang You, Xuemei Chen
MicroRNAs (miRNAs) are a central player in post-transcriptional regulation of gene expression and are involved in numerous biological processes in eukaryotes. Knowledge of the origins and divergence of miRNAs paves the way for a better understanding of the complexity of the regulatory networks that they participate in. The biogenesis, degradation, and regulatory activities of miRNAs are relatively better understood, but the evolutionary history of miRNAs still needs more exploration. Inverted duplication of target genes, random hairpin sequences and small transposable elements constitute three main models that explain the origination of miRNA genes (MIR)...
February 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28027512/shaping-plant-development-through-the-snrk1-tor-metabolic-regulators
#20
REVIEW
Elena Baena-González, Johannes Hanson
SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment...
December 24, 2016: Current Opinion in Plant Biology
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