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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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Rescooped by Ali Taheri from Virology and Bioinformatics from Virology.ca
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The Hitchhiker’s Guide to Python! — The Hitchhiker's Guide to Python

The Hitchhiker’s Guide to Python! — The Hitchhiker's Guide to Python | Plant Genetics, NGS and Bioinformatics | Scoop.it

This opinionated guide exists to provide both novice and expert Python developers a best-practice handbook to the installation, configuration, and usage of Python on a daily basis.


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Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation

Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation | Plant Genetics, NGS and Bioinformatics | Scoop.it

Topical application of nucleic acids offers many potential therapeutic advantages for suppressing genes in the skin, and potentially for systemic gene delivery. However, the epidermal barrier typically precludes entry of gene-suppressing therapy unless the barrier is disrupted. We now show that spherical nucleic acid nanoparticle conjugates (SNA-NCs), gold cores surrounded by a dense shell of highly oriented, covalently immobilized siRNA, freely penetrate almost 100% of keratinocytes in vitro, mouse skin, and human epidermis within hours after application. Significantly, these structures can be delivered in a commercial moisturizer or phosphate-buffered saline, and do not require barrier disruption or transfection agents, such as liposomes, peptides, or viruses. SNA-NCs targeting epidermal growth factor receptor (EGFR), an important gene for epidermal homeostasis, are > 100-fold more potent and suppress longer than siRNA delivered with commercial lipid agents in cultured keratinocytes. Topical delivery of 1.5 uM EGFR siRNA (50 nM SNA-NCs) for 3 wk to hairless mouse skin almost completely abolishes EGFR expression, suppresses downstream ERK phosphorylation, and reduces epidermal thickness by almost 40%. Similarly, EGFR mRNA in human skin equivalents is reduced by 52% after 60 h of treatment with 25 nM EGFR SNA-NCs. Treated skin shows no clinical or histological evidence of toxicity. No cytokine activation in mouse blood or tissue samples is observed, and after 3 wk of topical skin treatment, the SNA structures are virtually undetectable in internal organs. SNA conjugates may be promising agents for personalized, topically delivered gene therapy of cutaneous tumors, skin inflammation, and dominant negative genetic skin disorders.

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Nature Communications: Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase (2013)

Nature Communications: Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase (2013) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Leguminous plants establish a symbiosis with rhizobia to enable nitrogen fixation in root nodules under the control of the presumed root-to-shoot-to-root negative feedback called autoregulation of nodulation. In Lotus japonicus, autoregulation is mediated by CLE-RS genes that are specifically expressed in the root, and the receptor kinase HAR1 that functions in the shoot. However, the mature functional structures of CLE-RS gene products and the molecular nature of CLE-RS/HAR1signalling governed by these spatially distant components remain elusive. Here we show that CLE-RS2 is a post-translationally arabinosylated glycopeptide derived from the CLE domain. Chemically synthesized CLE-RS glycopeptides cause significant suppression of nodulation and directly bind to HAR1 in an arabinose-chain and sequence-dependent manner. In addition, CLE-RS2 glycopeptide specifically produced in the root is found in xylem sap collected from the shoot. We propose that CLE-RS glycopeptides are the long sought mobile signals responsible for the initial step of autoregulation of nodulation.


Via Kamoun Lab @ TSL
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Ice-Cap: A Method for Growing Arabidopsis and Tomato… | JoVE Video

Ice-Cap: A Method for Growing Arabidopsis and Tomato… | JoVE Video | Plant Genetics, NGS and Bioinformatics | Scoop.it
The Ice-Cap method allows one to grow plants in 96-well plates and non-destructively harvest root tissue from each seedling. DNA extracted from this root...
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Genetic modification; the development of transgenic ornamental plant varieties - Chandler - 2012 - Plant Biotechnology Journal - Wiley Online Library

Genetic modification; the development of transgenic ornamental plant varieties - Chandler - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plant transformation technology (hereafter abbreviated to GM, or genetic modification) has been used to develop many varieties of crop plants, but only a few varieties of ornamental plants. This disparity in the rate and extent of commercialisation, which has been noted for more than a decade, is not because there are no useful traits that can be engineered into ornamentals, is not due to market potential and is not due to a lack of research and development activity. The GM ornamental varieties which have been released commercially have been accepted in the marketplace. In this article, progress in the development of transgenic ornamentals is reviewed and traits useful to both consumers and producers are identified. In considering possible factors limiting the release of genetically modified ornamental products it is concluded that the most significant barrier to market is the difficulty of managing, and the high cost of obtaining, regulatory approval.

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Controlling genes with light - MIT News Office

Controlling genes with light - MIT News Office | Plant Genetics, NGS and Bioinformatics | Scoop.it
New technique can rapidly turn genes on and off, helping scientists better understand their function.

Shining light on genes

The new system consists of several components that interact with each other to control the copying of DNA into messenger RNA (mRNA), which carries genetic instructions to the rest of the cell. The first is a DNA-binding protein known as a transcription activator-like effector (TALE). TALEs are modular proteins that can be strung together in a customized way to bind any DNA sequence.

Fused to the TALE protein is a light-sensitive protein called CRY2 that is naturally found in Arabidopsis thaliana, a small flowering plant. When light hits CRY2, it changes shape and binds to its natural partner protein, known as CIB1. To take advantage of this, the researchers engineered a form of CIB1 that is fused to another protein that can either activate or suppress gene copying.

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eQTL Mapping Using RNA-seq Data | RNA-Seq Blog

eQTL Mapping Using RNA-seq Data | RNA-Seq Blog | Plant Genetics, NGS and Bioinformatics | Scoop.it
As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using
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U of G Project Receives Genome Canada Funding | University of Guelph

RT @UofGResearch: UofG researchers tackling one of the largest challenges in plant genetics thanks to @ontariogenomics @GenomeCanada http://t.co/L99zZCsGIk
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List of Bioinformatics Workshops and Training Resources

List of Bioinformatics Workshops and Training Resources | Plant Genetics, NGS and Bioinformatics | Scoop.it
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Why Not Make Fuel From CO2 In The Atmosphere? - Science 2.0

Why Not Make Fuel From CO2 In The Atmosphere? - Science 2.0 | Plant Genetics, NGS and Bioinformatics | Scoop.it
ScienceBlog.com
Why Not Make Fuel From CO2 In The Atmosphere?
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Accuracy of RNA-Seq and its dependence on sequencing depth

Accuracy of RNA-Seq and its dependence on sequencing depth | Plant Genetics, NGS and Bioinformatics | Scoop.it
Background

The cost of DNA sequencing has undergone a dramatical reduction in the past decade. As a result, sequencing technologies have been increasingly applied to genomic research. RNA-Seq is becoming a common technique for surveying gene expression based on DNA sequencing. As it is not clear how increased sequencing capacity has affected measurement accuracy of mRNA, we sought to investigate that relationship.

Result

We empirically evaluate the accuracy of repeated gene expression measurements using RNA-Seq. We identify library preparation steps prior to DNA sequencing as the main source of error in this process. Studying three datasets, we show that the accuracy indeed improves with the sequencing depth. However, the rate of improvement as a function of sequence reads is generally slower than predicted by the binomial distribution. We therefore used the beta-binomial distribution to model the overdispersion. The overdispersion parameters we introduced depend explicitly on the number of reads so that the resulting statistical uncertainty is consistent with the empirical data that measurement accuracy increases with the sequencing depth. The overdispersion parameters were determined by maximizing the likelihood. We shown that our modified beta-binomial model had lower false discovery rate than the binomial or the pure beta-binomial models.

Conclusion

We proposed a novel form of overdispersion guaranteeing that the accuracy improves with sequencing depth. We demonstrated that the new form provides a better fit to the data.

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Trends in Genetics - Population genetics of genomics-based crop improvement methods

Trends in Genetics - Population genetics of genomics-based crop improvement methods | Plant Genetics, NGS and Bioinformatics | Scoop.it

Many genome-wide association studies (GWAS) in humans are concluding that, even with very large sample sizes and high marker densities, most of the genetic basis of complex traits may remain unexplained. At the same time, recent research in plant GWAS is showing much greater success with fewer resources. Both GWAS and genomic selection (GS), a method for predicting phenotypes by the use of genome-wide marker data, are receiving considerable attention among plant breeders. In this review we explore how differences in population genetic histories, as well as past selection for traits of interest, have produced trait architectures and patterns of linkage disequilibrium (LD) that frequently differ dramatically between domesticated plants and humans, making detection of quantitative trait loci (QTL) effects in crops more rewarding and less costly than in humans.

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Next-generation transcriptome assembly

Next-generation transcriptome assembly | Plant Genetics, NGS and Bioinformatics | Scoop.it

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches — reference-based, de novo and combined strategies — along with some perspectives on transcriptome assembly in the near future.

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Mechanism for the endocytosis of spherical nucleic acid nanoparticle conjugates

Mechanism for the endocytosis of spherical nucleic acid nanoparticle conjugates | Plant Genetics, NGS and Bioinformatics | Scoop.it

Intracellular delivery of nucleic acids as gene regulation agents typically requires the use of cationic carriers or viral vectors, yet issues related to cellular toxicity or immune responses hamper their attractiveness as therapeutic candidates. The discovery that spherical nucleic acids (SNAs), polyanionic structures comprised of densely packed, highly oriented oligonucleotides covalently attached to the surface of nanoparticles, can effectively enter more than 50 different cell types presents a potential strategy for overcoming the limitations of conventional transfection agents. Unfortunately, little is known about the mechanism of endocytosis of SNAs, including the pathway of entry and specific proteins involved. Here, we demonstrate that the rapid cellular uptake kinetics and intracellular transport of SNAs stem from the arrangement of oligonucleotides into a 3D architecture, which supports their targeting of class A scavenger receptors and endocytosis via a lipid-raft–dependent, caveolae-mediated pathway. These results reinforce the notion that SNAs can serve as therapeutic payloads and targeting structures to engage biological pathways not readily accessible with linear oligonucleotides.

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A Tokyo Design Firm Made Artificial Human Organs for the Post-Apocalypse

A Tokyo Design Firm Made Artificial Human Organs for the Post-Apocalypse | Plant Genetics, NGS and Bioinformatics | Scoop.it

Once that great apocalyptic event—contagion, climate change, nuclear holocaust, zombies, whatever—drowns out the huddled masses of humanity, we can take solace in at least one thing: those who remain will have no shortage of suggestions from art and pop culture as to how best to carry on.

If it's a zombie scenario, they could, for instance, go Walking Dead and form a scrappy band and shack up in a prison. If it's disease, they could hack their bodies, adding Matt-Damon-in-Elysium-style cyborg arm implants to do combat with the rich. If it's rising sea levels, they could follow one Tokyo design firm's advice, and outfit themselves with artificial organs designed to make the human body more water-efficient. 


Via Szabolcs Kósa
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Plant Physiology: Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants

Plant Physiology: Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants | Plant Genetics, NGS and Bioinformatics | Scoop.it

Phytoplasmas are insect-transmitted bacterial plant pathogens and cause considerable damage to a diverse range of agricultural crops globally. Symptoms induced in infected plants suggest that these phytopathogens may modulate developmental processes within the plant host. We report herein that Aster Yellows phytoplasma strain Witches’ Broom (AY-WB) readily infects the model plant Arabidopsis thaliana ecotype Col-0, inducing symptoms that are characteristic of phytoplasma infection, such as the production of green leaf-like flowers (virescence and phyllody) and increased formation of stems and branches (witches' broom). We found that the majority of 56 genes encoding secreted AY-WB proteins (SAPs), which are candidate effector proteins, are expressed in Arabidopsis and the AY-WB insect vector Macrosteles quadrilineatus (Hemiptera; Cicadellidae). To identify which of these effector proteins induce symptoms of phyllody and virescence, we individually expressed the effector genes in Arabidopsis. From this screen, we have identified a novel AY-WB effector protein SAP54 that alters floral development, resulting in the production of leaf-like flowers that are similar to those produced by plants infected with this phytoplasma. This study offers novel insight into the effector profile of an insect-transmitted plant pathogen, and reports the first example of a microbial pathogen effector protein that targets flower development in a host.


Via Kamoun Lab @ TSL
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iTILLING: A Personalized Approach to the Identification of Induced Mutations in Arabidopsis

iTILLING: A Personalized Approach to the Identification of Induced Mutations in Arabidopsis | Plant Genetics, NGS and Bioinformatics | Scoop.it

TILLING (for Targeting Induced Local Lesions IN Genomes) is a well-established method for identifying plants carrying point mutations in genes of interest. A traditional TILLING project requires a significant investment of time and resources to establish the mutant population and screening infrastructure. Here, we describe a modified TILLING procedure that substantially reduces the investment needed to perform mutation screening. Our motivation for developing iTILLING was to make it practical for individual laboratories to rapidly perform mutation screens using specialized genetic backgrounds. With iTILLING, M2 seeds are collected in bulk from the mutagenized population of plants, greatly reducing the labor needed to manage the mutant lines. Growth of the M2 seedlings for mutation screening, tissue collection, and DNA extraction are all performed in 96-well format. Mutations are then identified using high-resolution melt-curve analysis of gene-specific polymerase chain reaction products. Individual plants carrying mutations of interest are transferred from the 96-well growth plates to soil. One scientist can complete an iTILLING screen in less than 4 months. As a proof-of-principle test, we applied iTILLING to Arabidopsis (Arabidopsis thaliana) plants that were homozygous for the mekk1-1 (for MAPK/ERK kinase kinase 1) mutation and also carried a MEKK1 rescue construct. The goal of our screen was to identify mutations in the closely linked MEKK2 and MEKK3 loci. We obtained five mutations in MEKK2 and seven mutations in MEKK3, all located within 20 kb of the mekk1-1 T-DNA insertion. Using repeated iterations of the iTILLING process, mutations in three or more tandemly duplicated genes could be generated.

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TILLING in extremis - Wang - 2012 - Plant Biotechnology Journal - Wiley Online Library

TILLING in extremis - Wang - 2012 - Plant Biotechnology Journal - Wiley Online Library | Plant Genetics, NGS and Bioinformatics | Scoop.it

Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silicoprocedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.

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eQTL Mapping Using RNA-seq Data

eQTL Mapping Using RNA-seq Data | Plant Genetics, NGS and Bioinformatics | Scoop.it

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping.

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What Blogging on Bioinformatics Tells us about the World

What Blogging on Bioinformatics Tells us about the World | Plant Genetics, NGS and Bioinformatics | Scoop.it

Bioinformatics is a very young field of research. Its growth started in earnest after the publication of human genome, when many scientists saw immense medical value of such vast genetic data and decided to explore further. Thirteen years passed since then and the same message reached all parts of the world. Therefore checking how many people from around the globe are interested in bioinformatics today is possibly an indication of progress they are making in education and economic matters.

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The Arabidopsis embryo as a miniature morphogenesis model - Wendrich - 2013 - New Phytologist - Wiley Online Library

The Arabidopsis embryo as a miniature morphogenesis model - Wendrich - 2013 - New Phytologist - Wiley Online Library | Plant Genetics, NGS and Bioinformatics | Scoop.it

Four basic ingredients of morphogenesis, oriented cell division and expansion, cell–cell communication and cell fate specification allow plant cells to develop into a wide variety of organismal architectures. A central question in plant biology is how these cellular processes are regulated and orchestrated. Here, we present the advantages of the early Arabidopsis embryo as a model for studying the control of morphogenesis. All ingredients of morphogenesis converge during embryogenesis, and the highly predictable nature of embryo development offers unprecedented opportunities for understanding their regulation in time and space. In this review we describe the morphogenetic principles underlying embryo patterning and discuss recent advances in their regulation. Morphogenesis is under tight transcriptional control and most genes that were identified as important regulators of embryo patterning encode transcription factors or components of signaling pathways. There exists, therefore, a large gap between the transcriptional control of embryo morphogenesis and the cellular execution. We describe the first such connections, and propose future directions that should help bridge this gap and generate comprehensive understanding of the control of morphogenesis.

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Brazil, Canada and South Africa bullish on agbiotech

Brazil, Canada and South Africa bullish on agbiotech | Plant Genetics, NGS and Bioinformatics | Scoop.it

Transgenic crop plantings in developing countries surpassed those in industrial nations, with the former growing 52% of the world's transgenic varieties. Although the United States dominates overall, transgenic acreage in Brazil, Canada and South Africa continued double-digit growth. Elsewhere, Sudan and Cuba planted their first transgenic crops (Bt cotton and Bt maize, respectively). Europe continues to wind down its field trials; Germany and Sweden withdrew the low-starch Amflora transgenic potato from the market.

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Caltech chemists think they've cracked photosynthesis

Caltech chemists think they've cracked photosynthesis | Plant Genetics, NGS and Bioinformatics | Scoop.it
Chemists at the California Institute of Technology (Caltech) and the Lawrence Berkeley National Laboratory believe they can now explain one of the remaining mysteries of photosynthesis, the chemica...
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Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement : Nature Biotechnology : Nature Publishing Group

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement : Nature Biotechnology : Nature Publishing Group | Plant Genetics, NGS and Bioinformatics | Scoop.it
A draft sequence of the staple crop kabuli chickpea, together with resequencing and analysis of 90 additional lines from 10 countries, provides a resource for breeders.

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

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FAO: The Youth Guide to Biodiversity

FAO: The Youth Guide to Biodiversity | Plant Genetics, NGS and Bioinformatics | Scoop.it

Wow - nice resource! A 260 page PDF from Youth and United Nationsl Global Alliance (YUNGA http://yunga-youth.weebly.com/). Beautiful design and full of case studies and definations and links - plant and animal examples! Ch 9 is "In farmers' fields: biodiversity and agriculture".


Via Mary Williams
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