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Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes | Plant Genetics, NGS and Bioinformatics | Scoop.it

We take a comprehensive approach to the study of regulatory control of gene expression in melanocytes that proceeds from large-scale enhancer discovery facilitated by ChIP-seq; to rigorous validation in silico, in vitro, and in vivo; and finally to the use of machine learning to elucidate a regulatory vocabulary with genome-wide predictive power. We identify 2489 putative melanocyte enhancer loci in the mouse genome by ChIP-seq for EP300 and H3K4me1. We demonstrate that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression in melanocytes in culture (86%; 43/50) and in transgenic zebrafish (70%; 7/10). Next, using the sequences of these putative enhancers as a training set for a supervised machine learning algorithm, we develop a vocabulary of 6-mers predictive of melanocyte enhancer function. Lastly, we demonstrate that this vocabulary has genome-wide predictive power in both the mouse and human genomes. This study provides deep insight into the regulation of gene expression in melanocytes and demonstrates a powerful approach to the investigation of regulatory sequences that can be applied to other cell types.

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Plant Genetics, NGS and Bioinformatics
Papers and topics in plant genetics, NGS and bioinformatics
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DNA editing takes a serious step forward -- for better or worse

DNA editing takes a serious step forward -- for better or worse | Plant Genetics, NGS and Bioinformatics | Scoop.it
It's a scenario that has haunted biologists since the dawn of the DNA age: the evil scientist custom-crafting a human being with test tubes and Petri dishes.
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High-throughput functional genomics using CRISPR-Cas9. - PubMed - NCBI

High-throughput functional genomics using CRISPR-Cas9. - PubMed - NCBI | Plant Genetics, NGS and Bioinformatics | Scoop.it

Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.

Nat Rev Genet. 2015 May;16(5):299-311. doi: 10.1038/nrg3899. Epub 2015 Apr 9.

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Efficiency of CRISPR-Cas9 Genome Editing Tool is Increased Eightfold

Efficiency of CRISPR-Cas9 Genome Editing Tool is Increased Eightfold | Plant Genetics, NGS and Bioinformatics | Scoop.it
Researchers at the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch and the Berlin Institute of Health (BIH) have engineered a more
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Are we ready for back-to-nature crop breeding?: Trends in Plant Science

Are we ready for back-to-nature crop breeding?: Trends in Plant Science | Plant Genetics, NGS and Bioinformatics | Scoop.it

Sustainable agriculture in response to increasing demands for food depends on development of high-yielding crops with high nutritional value that require minimal intervention during growth. To date, the focus has been on changing plants by introducing genes that impart new properties, which the plants and their ancestors never possessed. By contrast, we suggest another potentially beneficial and perhaps less controversial strategy that modern plant biotechnology may adopt. This approach, which broadens earlier approaches to reverse breeding, aims to furnish crops with lost properties that their ancestors once possessed in order to tolerate adverse environmental conditions. What molecular techniques are available for implementing such rewilding? Are the strategies legally, socially, economically, and ethically feasible? These are the questions addressed in this review.

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One hundred important questions facing plant science research - Grierson - 2011 - New Phytologist - Wiley Online Library

One hundred important questions facing plant science research - Grierson - 2011 - New Phytologist - Wiley Online Library | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plant science has never been more important. The growing and increasingly prosperous human population needs abundant safe and nutritious food, shelter, clothes, fibre, and renewable energy, and needs to address the problems generated by climate change, while preserving habitats. These global challenges can only be met in the context of a strong fundamental understanding of plant biology and ecology, and translation of this knowledge into field-based solutions.

Plant science is beginning to address these grand challenges, but it is not clear that the full range of challenges facing plant science is known or has been assessed. What questions should the next generation of plant biologists be addressing? To start to answer this question we set out to compile a list of 100 important questions facing plant science research.

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The amazing decline of global hunger, in one chart

The amazing decline of global hunger, in one chart | Plant Genetics, NGS and Bioinformatics | Scoop.it

hunger is on a major decline in the world. Since 1990, there's been a sustained and massive collapse in the number of people who have difficulty accessing food.


Via CIMMYT, Int.
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Frontiers: The past, present and future of breeding rust resistant wheat (2014)

Frontiers: The past, present and future of breeding rust resistant wheat (2014) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Two classes of genes are used for breeding rust resistant wheat. The first class, called R (for resistance) genes, are pathogen race-specific in their action, effective at all plant growth stages and probably mostly encode immune receptors of the nucleotide binding leucine rich repeat (NB-LRR) class. The second class called Adult Plant Resistance genes (APR) because resistance is usually functional only in adult plants, and, in contrast to most R genes, the levels of resistance conferred by single APR genes are only partial and allow considerable disease development. Some but not all APR genes provide resistance to all isolates of a rust pathogen species and a subclass of these provides resistance to several fungal pathogen species. Initial indications are that APR genes encode a more heterogeneous range of proteins than R proteins. Two APR genes, Lr34 and Yr36, have been cloned from wheat and their products are an ABC transporter and a protein kinase, respectively. Lr34 and Sr2 have provided long lasting and widely used (durable) partial resistance and are mainly used in conjunction with other R and APR genes to obtain adequate rust resistance. We caution that some APR genes indeed include race-specific, weak R genes which may be of the NB-LRR class. A research priority to better inform rust resistance breeding is to characterize further APR genes in wheat and to understand how they function and how they interact when multiple APR and R genes are stacked in a single genotype by conventional and GM breeding. An important message is do not be complacent about the general durability of all APR genes.


Via Kamoun Lab @ TSL
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What is the World's Biggest Cash Crop? - Information Is Beautiful

What is the World's Biggest Cash Crop? - Information Is Beautiful | Plant Genetics, NGS and Bioinformatics | Scoop.it
Rice? Wheat? Maize? Soya? What's the world's biggest cash crop? The answer might surprise you.

Via Mary Williams
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Building agricultural research

Building agricultural research | Plant Genetics, NGS and Bioinformatics | Scoop.it

Nine billion people are expected to inhabit Planet Earth by 2050. Without agricultural research, there is little hope of sustaining this population surge, given that arable land and water supplies are fixed commodities. Yet for decades the agricultural sector has suffered from neglect. If we want to combat new strains of pests that destroy crops, find new crop varieties enriched in nutritional value, improve yields, develop resistance to disease and drought, and provide environmentally sensitive cultivation practices, then agricultural research must be a priority. Why isn't it?

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A faster Rubisco with potential to increase photosynthesis in crops

A faster Rubisco with potential to increase photosynthesis in crops | Plant Genetics, NGS and Bioinformatics | Scoop.it

In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere1. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants2, 3. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield4, 5, 6. However, the complex nature of Rubisco’s assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful7, 8. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains9, 10. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes11, 12. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins

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Rescooped by Ali Taheri from Publications from The Sainsbury Laboratory
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Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014)

Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Via The Sainsbury Lab
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The Sainsbury Lab's curator insight, September 18, 2014 4:52 AM

The CRISPR/Cas9 system is highly efficient at generating targeted mutations in stable transgenic tomato plants, and homozygous deletions of a desired size can be created in the first generation.

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Silencing the mob: disrupting quorum sensing as a means to fight plant disease

Silencing the mob: disrupting quorum sensing as a means to fight plant disease | Plant Genetics, NGS and Bioinformatics | Scoop.it

Bacteria are able to sense their population's density through a cell–cell communication system, termed ‘quorum sensing’ (QS). This system regulates gene expression in response to cell density through the constant production and detection of signalling molecules. These molecules commonly act as auto-inducers through the up-regulation of their own synthesis. Many pathogenic bacteria, including those of plants, rely on this communication system for infection of their hosts. The finding that the countering of QS-disrupting mechanisms exists in many prokaryotic and eukaryotic organisms offers a promising novel method to fight disease. During the last decade, several approaches have been proposed to disrupt QS pathways of phytopathogens, and hence to reduce their virulence. Such studies have had varied success in vivo, but most lend promising support to the idea that QS manipulation could be a potentially effective method to reduce bacterial-mediated plant disease. This review discusses the various QS-disrupting mechanisms found in both bacteria and plants, as well as the different approaches applied artificially to interfere with QS pathways and thus protect plant health.


Via Jennifer Mach
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Nature Biotechnology: Wheat rescued from fungal disease (2014)

Nature Biotechnology: Wheat rescued from fungal disease (2014) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Knockout of all six alleles of a gene in the large wheat genome confers resistance to powdery mildew --- Genetic engineering to improve crops is entering a new era as conventional transgenesis technology, which involves random insertion of genes into the genome, is superseded by newer approaches that enable precise genetic alterations. A particular technological challenge in carrying out targeted genome modification in crops is that many plant genomes are polyploid, including such important species as wheat, potato and canola1. In this issue, Wang et al.2 report engineering of the hexaploid wheat genome using sequence-specific nucleases (SSNs)—the first demonstration in a polyploid crop of SSN-mediated genetic alterations that are stably transmitted to the next generation. By knocking out all six alleles encoding the MILDEW-RESISTANCE LOCUS (MLO) protein, the authors generated a mutant line that shows strong resistance to powdery mildew, a devastating fungal disease. This is a remarkable feat, given the ploidy and enormous size (17.1 Gb) of the wheat genome, and showcases the power of SSNs for engineering complex plant genomes and for creating crops with valuable traits.


Via Kamoun Lab @ TSL, Francis Martin
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A Gene-Edited Potato | MIT Technology Review

A Gene-Edited Potato | MIT Technology Review | Plant Genetics, NGS and Bioinformatics | Scoop.it
Plant scientists can swiftly modify crops in ways that would take years with conventional breeding.

Dan Voytas is a plant geneticist at the University of Minnesota. But two days a week he stops studying the fundamentals of DNA engineering and heads to a nearby company called Cellectis Plant Sciences, where he applies them.

His newest creation, described in a plant journal this month, is a Ranger Russet potato that doesn’t accumulate sweet sugars at typical cold storage temperatures. That will let it last longer, and when it’s fried it won’t produce as much acrylamide, a suspected carcinogen.

What’s different about the potato is that it was bred with the help of gene editing, a new kind of technique for altering DNA that plant scientists say is going to be revolutionary for its simplicity and power. The technology could also be a way to engineer plants that avoid the stigma, and the regulations, normally associated with genetically modified organisms (GMOs).

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Sweet potato naturally 'genetically modified'

Sweet potato naturally 'genetically modified' | Plant Genetics, NGS and Bioinformatics | Scoop.it
Sweet potatoes from all over the world naturally contain genes from the bacterium Agrobacterium, researchers report. Sweet potato is one of the most important food crops for human consumption in the world. Because of the presence of this "foreign" DNA, sweet potato can be seen as a "natural GMO," the researchers say.
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Sequencing consolidates molecular markers with plant breeding practice

Sequencing consolidates molecular markers with plant breeding practice | Plant Genetics, NGS and Bioinformatics | Scoop.it
Key message

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.

Abstract

The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.

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Regulatory uncertainty over genome editing - Nature Plants

Regulatory uncertainty over genome editing - Nature Plants | Plant Genetics, NGS and Bioinformatics | Scoop.it

Jones 2015

Genome editing opens up opportunities for the precise and rapid alteration of crops to boost yields, protect against pests and diseases and enhance nutrient content. The extent to which applied plant research and crop breeding benefit will depend on how the EU decides to regulate this fledgling technology.

 


Via dromius, Guogen Yang
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Methods in Enzymology Vol 546 - The Use of CRISPR/Cas9, ZFNs and TALENs in Generating Site-Specific Genome Alterations

Methods in Enzymology Vol 546 - The Use of CRISPR/Cas9, ZFNs and TALENs in Generating Site-Specific Genome Alterations | Plant Genetics, NGS and Bioinformatics | Scoop.it
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. Methods to assess mitochondrial function is of great interest to neuroscientists studying chronic forms of neurodegeneration, including Parkinson's, Alzheimer's, ALS, Huntington's and other triplet repeat diseases, but also to those working on acute conditions such as stroke and traumatic brain injury. This volume covers research methods on how to assess the life cycle of mitochondria including trafficking, fusion, fission, and degradation. Multiple perspectives on the complex and difficult problem of measurement of mitochondrial reactive oxygen species production with fluorescent indicators and techniques ranging in scope from measurements on isolated mitochondria to non-invasive imaging of metabolic function.Continues the legacy of this premier serial with quality chapters authored by leaders in the fieldCovers research methods in biomineralization scienceProvides invaluable details on state-of-the-art methods to assess a broad array of mitochondrial functions

Via dromius
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Making designer mutants in all kinds of model organisms

Making designer mutants in all kinds of model organisms | Plant Genetics, NGS and Bioinformatics | Scoop.it

Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability to analyze developmental processes using sophisticated designer genetic tools. Excitingly, these robust and simple genomic engineering tools also promise to revolutionize developmental studies using less well established experimental organisms.


Modern developmental biology was born out of the fruitful marriage between traditional embryology and genetics. Genetic tools, together with advanced microscopy techniques, serve as the most fundamental means for developmental biologists to elucidate the logistics and the molecular control of growth, differentiation and morphogenesis. For this reason, model organisms with sophisticated and comprehensive genetic tools have been highly favored for developmental studies. Advances made in developmental biology using these genetically amenable models have been well recognized. The Nobel prize in Physiology or Medicine was awarded in 1995 to Edward B. Lewis, Christiane Nüsslein-Volhard and Eric F. Wieschaus for their discoveries on the ‘Genetic control of early structural development’ usingDrosophila melanogaster, and again in 2002 to John Sulston, Robert Horvitz and Sydney Brenner for their discoveries of ‘Genetic regulation of development and programmed cell death’ using the nematode worm Caenorhabditis elegans. These fly and worm systems remain powerful and popular models for invertebrate development studies, while zebrafish (Danio rerio), the dual frog species Xenopus laevis and Xenopus tropicalis, rat (Rattus norvegicus), and particularly mouse (Mus musculus) represent the most commonly used vertebrate model systems. To date, random or semi-random mutagenesis (‘forward genetic’) approaches have been extraordinarily successful at advancing the use of these model organisms in developmental studies. With the advent of reference genomic data, however, sequence-specific genomic engineering tools (‘reverse genetics’) enable targeted manipulation of the genome and thus allow previously untestable hypotheses of gene function to be addressed.


Via Dr. Stefan Gruenwald, Mary Williams
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Unit 1 of English Communication for Scientists | Learn Science at Scitable

Unit 1 of English Communication for Scientists | Learn Science at Scitable | Plant Genetics, NGS and Bioinformatics | Scoop.it

Communication is an integral part of the research you perform as a scientist. Your written papers serve as a gauge of your scientific productivity and provide a long-lasting body of knowledge from which other scientists can build their research. The oral presentations you deliver make your latest research known to the community, helping your peers stay up to date. Discussions enable you to exchange ideas and points of view. Letters, memos, and résumés help you build and maintain relationships with colleagues, suppliers, employers, and so on.

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The top 100 papers: NATURE magazine explores the most-cited research papers of all time

The top 100 papers: NATURE magazine explores the most-cited research papers of all time | Plant Genetics, NGS and Bioinformatics | Scoop.it

The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating — all of these breakthroughs won Nobel prizes and international acclaim. Yet none of the papers that announced them comes anywhere close to ranking among the 100 most highly cited papers of all time.

 

Citations, in which one paper refers to earlier works, are the standard means by which authors acknowledge the source of their methods, ideas and findings, and are often used as a rough measure of a paper’s importance. Fifty years ago, Eugene Garfield published the Science Citation Index (SCI), the first systematic effort to track citations in the scientific literature. To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. (See the full list at Web of Science Top 100.xls or the interactive graphic, below.) The search covered all of Thomson Reuter’s Web of Science, an online version of the SCI that also includes databases covering the social sciences, arts and humanities, conference proceedings and some books. It lists papers published from 1900 to the present day.

 

The exercise revealed some surprises, not least that it takes a staggering 12,119 citations to rank in the top 100 — and that many of the world’s most famous papers do not make the cut. A few that do, such as the first observation1 of carbon nanotubes (number 36) are indeed classic discoveries. But the vast majority describe experimental methods or software that have become essential in their fields.

 

The most cited work in history, for example, is a 1951 paper2 describing an assay to determine the amount of protein in a solution. It has now gathered more than 305,000 citations — a recognition that always puzzled its lead author, the late US biochemist Oliver Lowry.


Via Dr. Stefan Gruenwald
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Here's Why We Haven't Quite Figured Out How to Feed Billions More People

Here's Why We Haven't Quite Figured Out How to Feed Billions More People | Plant Genetics, NGS and Bioinformatics | Scoop.it
Solving the world's looming food crisis will require big investments in agricultural research, yet public support for that is lagging.

Via Mary Williams, Loïc Lepiniec
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Should we upgrade photosynthesis and grow supercrops? - opinion - 06 October 2014 - New Scientist

Should we upgrade photosynthesis and grow supercrops? - opinion - 06 October 2014 - New Scientist | Plant Genetics, NGS and Bioinformatics | Scoop.it
A long-awaited breakthrough by crop scientists raises some thorny issues for conservation. Michael Le Page proposes a radical solution
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GMOs Are Old Hat. Synthetically Modified Food Is The New Frontier

GMOs Are Old Hat. Synthetically Modified Food Is The New Frontier | Plant Genetics, NGS and Bioinformatics | Scoop.it
Scientists hyping synthetic biology say it may one day give us biofuels, drugs and organisms that will solve hefty global problems. But synthetic biology food is already here, and causing controversy.
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Nature communications: Niche and host-associated functional signatures of the root surface microbiome

Nature communications: Niche and host-associated functional signatures of the root surface microbiome | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.


Via Stéphane Hacquard, Francis Martin
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