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Scientists uncover mechanism by which plants inherit epigenetic modifications

Scientists uncover mechanism by which plants inherit epigenetic modifications | Plant Genetics, NGS and Bioinformatics | Scoop.it
Scientists have discovered that epigenetic modifications can be inherited in pollen and that this process is guided by small RNA. By this mechanism, acquired traits can be inherited over many hundreds of generations.
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Plant Genetics, NGS and Bioinformatics
Papers and topics in plant genetics, NGS and bioinformatics
Curated by Ali Taheri
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TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline | Plant Genetics, NGS and Bioinformatics | Scoop.it

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, tassel-gbs, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The tassel-gbs pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8–16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished “pseudo-reference” consisting of numerous contigs. We describe the tassel-gbs pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the tassel-gbs pipeline provide robust tools for studying genomic diversity.

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Opportunities in plant synthetic biology

Opportunities in plant synthetic biology | Plant Genetics, NGS and Bioinformatics | Scoop.it

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

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Natural Variations and Genome-Wide Association Studies in Crop Plants - Annual Review of Plant Biology, 65(1):

Natural Variations and Genome-Wide Association Studies in Crop Plants - Annual Review of Plant Biology, 65(1): | Plant Genetics, NGS and Bioinformatics | Scoop.it

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencingbased genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.

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Male Sterility and Fertility Restoration in Crops - Annual Review of Plant Biology, 65(1):

Male Sterility and Fertility Restoration in Crops - Annual Review of Plant Biology, 65(1): | Plant Genetics, NGS and Bioinformatics | Scoop.it

In plants, male sterility can be caused either by mitochondrial genes with coupled nuclear genes or by nuclear genes alone; the resulting conditions are known as cytoplasmic male sterility (CMS) and genic male sterility (GMS), respectively. CMS and GMS facilitate hybrid seed production for many crops and thus allow breeders to harness yield gains associated with hybrid vigor (heterosis). In CMS, layers of interaction between mitochondrial and nuclear genes control its male specificity, occurrence, and restoration of fertility. Environment-sensitive GMS (EGMS) mutants may involve epigenetic control by noncoding RNAs and can revert to fertility under different growth conditions, making them useful breeding materials in the hybrid seed industry. Here, we review recent research on CMS and EGMS systems in crops, summarize general models of male sterility and fertility restoration, and discuss the evolutionary significance of these reproductive systems.

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Programmable bacteria detect and record an environmental signal in the mammalian gut

The human microbiota represents the trillions of bacteria that live on the skin, in the oral, nasal, and aural cavities, and throughout the gastrointestinal tract. The species that live in the gastrointestinal tract, the gut microbiota, closely interact with host cells and have a profound impact on health. To develop tools to effectively monitor the gut microbiota and ultimately help in disease diagnosis, we have engineered Escherichia coli to sense and record environmental stimuli, and demonstrated that E. coli with such memory systems can survive and function in the mammalian gut. This work demonstrates that E. coli can be engineered into living diagnostics capable of nondestructively probing the mammalian gut.

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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations | Plant Genetics, NGS and Bioinformatics | Scoop.it
Abstract

We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

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Almost all steps of NGS library preparation protocols introduce bias, especially in the case of RNA-Seq | RNA-Seq Blog

Almost all steps of NGS library preparation protocols introduce bias, especially in the case of RNA-Seq | RNA-Seq Blog | Plant Genetics, NGS and Bioinformatics | Scoop.it
Next-generation sequencing (NGS) has caused a revolution in biology. NGS requires the preparation of libraries in which (fragments of) DNA or RNA molecules are
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PLOS Biology: A Field Guide to Genomics Research

PLOS Biology: A Field Guide to Genomics Research | Plant Genetics, NGS and Bioinformatics | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) Assembly - Curr. Protoc. Mol. Biol.

Reyon et al, 2014

Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput.


Via dromius
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The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana | Plant Genetics, NGS and Bioinformatics | Scoop.it

Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ∼25–50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs.

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Current Opinion in Biotechnology: Metabolic potential of endophytic bacteria (2013)

Current Opinion in Biotechnology: Metabolic potential of endophytic bacteria (2013) | Plant Genetics, NGS and Bioinformatics | Scoop.it

The bacterial endophytic microbiome promotes plant growth and health and beneficial effects are in many cases mediated and characterized by metabolic interactions. Recent advances have been made in regard to metabolite production by plant microsymbionts showing that they may produce a range of different types of metabolites. These substances play a role in defense and competition, but may also be needed for specific interaction and communication with the plant host. Furthermore, few examples of bilateral metabolite production are known and endophytes may modulate plant metabolite synthesis as well. We have just started to understand such metabolic interactions between plants and endophytes, however, further research is needed to more efficiently make use of beneficial plant-microbe interactions and to reduce pathogen infestation as well as to reveal novel bioactive substances of commercial interest.


Via Jean-Michel Ané, Kamoun Lab @ TSL, Aigli Espera
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‘Duon’ controversy: Scientists claim second code hiding within DNA, provoking sharp rebuke | Genetic Literacy Project

‘Duon’ controversy: Scientists claim second code hiding within DNA, provoking sharp rebuke | Genetic Literacy Project | Plant Genetics, NGS and Bioinformatics | Scoop.it
In a claim sharply challenged as overhyped, University of Washington scientists say they have discovered a second code hiding within DNA that could change how we read the instructions contained in DNA that help us make sense of health and disease.
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GMOs vs. mutagenesis vs. conventional breeding: Which wins?

GMOs vs. mutagenesis vs. conventional breeding: Which wins? | Plant Genetics, NGS and Bioinformatics | Scoop.it
Is the process of mutagenesis more safe and efficient than genetic modification? Maybe not.
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Bacterial tricks for turning plants into zombies

Bacterial tricks for turning plants into zombies | Plant Genetics, NGS and Bioinformatics | Scoop.it
Microbe deploys proteins that manipulate both the plant it infects and the insects that spread it.
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rougeforfire's curator insight, April 9, 2:15 AM

So you say taht zombies do exist and that there are pant zombies... So plants vs. zombies was a lie !!

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The Cell Biology of Cellulose Synthesis - Annual Review of Plant Biology, 65(1):

The Cell Biology of Cellulose Synthesis - Annual Review of Plant Biology, 65(1): | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plant stature and development are governed by cell proliferation and directed cell growth. These parameters are determined largely by cell wall characteristics. Cellulose microfibrils, composed of hydrogen-bonded β-1,4 glucans, are key components for anisotropic growth in plants. Cellulose is synthesized by plasma membrane–localized cellulose synthase complexes. In higher plants, these complexes are assembled into hexagonal rosettes in intracellular compartments and secreted to the plasma membrane. Here, the complexes typically track along cortical microtubules, which may guide cellulose synthesis, until the complexes are inactivated or internalized. Determining the regulatory aspects that control the behavior of cellulose synthase complexes is vital to understanding directed cell and plant growth and to tailoring cell wall content for industrial products, including paper, textiles, and fuel. In this review, we summarize and discuss cellulose synthesis and regulatory aspects of the cellulose synthase complex, focusing on Arabidopsis thaliana.

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Genetic Engineering and Breeding of Drought-Resistant Crops - Annual Review of Plant Biology, 65(1):

Genetic Engineering and Breeding of Drought-Resistant Crops - Annual Review of Plant Biology, 65(1): | Plant Genetics, NGS and Bioinformatics | Scoop.it

Drought is one of the most important environmental stresses affecting the productivity of most field crops. Elucidation of the complex mechanisms underlying drought resistance in crops will accelerate the development of new varieties with enhanced drought resistance. Here, we provide a brief review on the progress in genetic, genomic, and molecular studies of drought resistance in major crops. Drought resistance is regulated by numerous small-effect loci and hundreds of genes that control various morphological and physiological responses to drought. This review focuses on recent studies of genes that have been well characterized as affecting drought resistance and genes that have been successfully engineered in staple crops. We propose that one significant challenge will be to unravel the complex mechanisms of drought resistance in crops through more intensive and integrative studies in order to find key functional components or machineries that can be used as tools for engineering and breeding drought-resistant crops.

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Biotech Crop Development: From Idea to Product - Annual Review of Plant Biology

Biotech Crop Development: From Idea to Product - Annual Review of Plant Biology | Plant Genetics, NGS and Bioinformatics | Scoop.it

Genetically engineered crops were first commercialized in 1994 and since then have been rapidly adopted, enabling growers to more effectively manage pests and increase crop productivity while ensuring food, feed, and environmental safety. The development of these crops is complex and based on rigorous science that must be well coordinated to create a plant with desired beneficial phenotypes. This article describes the general process by which a genetically engineered crop is developed from an initial concept to a commercialized product.

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Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems | Plant Genetics, NGS and Bioinformatics | Scoop.it
ABSTRACT

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms.

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Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis | Plant Genetics, NGS and Bioinformatics | Scoop.it

Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera andArabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.

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BWA, SOAP, MAQ, BLAT...OMG Alignment Methods!

BWA, SOAP, MAQ, BLAT...OMG Alignment Methods! | Plant Genetics, NGS and Bioinformatics | Scoop.it

Via Niklaus Grunwald
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Niklaus Grunwald's curator insight, January 19, 10:24 AM

A brief primer of current aingment methods for short-read sequencing applciations comparin BWA, Bowtie, SOAP, BLAT, BLAST, and more.

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5 Unbelievable (but Real) Technologies Made Possible by Synthetic Biology - DailyFinance

5 Unbelievable (but Real) Technologies Made Possible by Synthetic Biology - DailyFinance | Plant Genetics, NGS and Bioinformatics | Scoop.it
Synthetic biology, or breaking down life into its basic component parts to create enhanced biological systems, can be likened to writing software
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A universal RNA extraction protocol for land plants | RNA-Seq Blog

A universal RNA extraction protocol for land plants | RNA-Seq Blog | Plant Genetics, NGS and Bioinformatics | Scoop.it
New method will facilitate next-generation sequencing and comparative studies of gene expression RNA, a nucleic acid involved in protein synthesis, is widely
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CRISPR technology leaps from lab to industry

CRISPR technology leaps from lab to industry | Plant Genetics, NGS and Bioinformatics | Scoop.it

Instead of taking prescription pills to treat their ailments, patients may one day opt for genetic 'surgery' — using an innovative gene-editing technology to snip out harmful mutations and swap in healthy DNA.
The system, called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), has exploded in popularity in the past year, with genetic engineers, neuroscientists and even plant biologists viewing it as a highly efficient and precise research tool. Now, the gene-editing system has spun out a biotechnology company that is attracting attention from investors as well.


Via Szabolcs Kósa
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MAKER-P: an annotation pipeline for plants | Kaboodle

MAKER-P: an annotation pipeline for plants | Kaboodle | Plant Genetics, NGS and Bioinformatics | Scoop.it

The popular MAKER annotation pipeline has been extended and optimised to allow the annotation of plant species:

Sequencing diverse plant species of evolutionary, agricultural, and medicinal interest is becoming routine for even small groups; genome annotation and analysis is much less so. The MAKER-P pipeline is designed to make the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes.

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Regulatory modules controlling maize inflorescence architecture

Abstract

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.

 
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