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Articles relating to my job in cereal bioinformatics and NGS related activities.
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Rescooped by Nathan Watson-Haigh from Plant evolution
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The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria

The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria | cereal bioinformatics | Scoop.it

C4 photosynthesis represents a most remarkable case of convergent evolution of a complex trait, which includes the reprogramming of the expression patterns of thousands of genes. Anatomical, physiological, and phylogenetic and analyses as well as computational modeling indicate that the establishment of a photorespiratory carbon pump (termed C2 photosynthesis) is a prerequisite for the evolution of C4. However, a mechanistic model explaining the tight connection between the evolution of C4 and C2 photosynthesis is currently lacking. Here we address this question through comparative transcriptomic and biochemical analyses of closely related C3, C3-C4, and C4 species, combined with Flux Balance Analysis constrained through a mechanistic model of carbon fixation. We show that C2 photosynthesis creates a misbalance in nitrogen metabolism between bundle sheath and mesophyll cells. Rebalancing nitrogen metabolism requires anaplerotic reactions that resemble at least parts of a basic C4 cycle. Our findings thus show how C2 photosynthesis represents a pre-adaptation for the C4 system, where the evolution of the C2 system establishes important C4 components as a side effect.


Via Pierre-Marc Delaux
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Rescooped by Nathan Watson-Haigh from MycorWeb Plant-Microbe Interactions
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A field guide to whole-genome sequencing, assembly and annotation

A field guide to whole-genome sequencing, assembly and annotation | cereal bioinformatics | Scoop.it

Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.


Via Francis Martin
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Scooped by Nathan Watson-Haigh
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Accuracy of MicroRNA Discovery Pipelines in Non-Model Organisms Using Closely Related Species Genomes

Accuracy of MicroRNA Discovery Pipelines in Non-Model Organisms Using Closely Related Species Genomes | cereal bioinformatics | Scoop.it
Mapping small reads to genome reference is an essential and more common approach to identify microRNAs (miRNAs) in an organism.
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Rescooped by Nathan Watson-Haigh from Structure and Evolution of Plant Genomes
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mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

The Plant Cell May 2014 vol. 26 no. 5 1878-1900


Via Frédéric Choulet
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Frédéric Choulet's curator insight, June 30, 12:18 PM

Nascent allohexaploid wheat may represent the initial genetic state of common wheat (Triticum aestivum), which arose as a hybrid between Triticum turgidum (AABB) and Aegilops tauschii (DD) and by chromosome doubling and outcompeted its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA transcriptome analyses in nascent allohexaploid wheat and its following generations, their progenitors, and the natural allohexaploid cultivar Chinese Spring, with the assistance of recently published A and D genome sequences. We found that nonadditively expressed protein-coding genes were rare but relevant to growth vigor. Moreover, a high proportion of protein-coding genes exhibited parental expression level dominance, with genes for which the total homoeolog expression level in the progeny was similar to that in T. turgidum potentially participating in development and those with similar expression to that in Ae. tauschii involved in adaptation. In addition, a high proportion of microRNAs showed nonadditive expression upon polyploidization, potentially leading to differential expression of important target genes. Furthermore, increased small interfering RNA density was observed for transposable element–associated D homoeologs in the allohexaploid progeny, which may account for biased repression of D homoeologs. Together, our data provide insights into small RNA–mediated dynamic homoeolog regulation mechanisms that may contribute to heterosis in nascent hexaploid wheat.

Rescooped by Nathan Watson-Haigh from Plant evolution
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Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines

Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines | cereal bioinformatics | Scoop.it

Summary

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novotranscriptome assembly. This led to the discovery of >2,400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.


Via Pierre-Marc Delaux
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Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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What is the extent of gender bias in bioinformatics? Please help me find out. - SEQanswers

What is the extent of gender bias in bioinformatics? Please help me find out. Bioinformatics (What is the extent of gender bias in bioinformatics? Please help me find out.

Via Mel Melendrez-Vallard
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Rescooped by Nathan Watson-Haigh from Bioinformatics, Comparative Genomics and Molecular Evolution
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Computational Biology Primers in Nature Biotechnology


Via Arjen ten Have
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Arjen ten Have's curator insight, April 14, 11:28 AM

Nice collection of links to primers!!

Rescooped by Nathan Watson-Haigh from The science toolbox
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Why do academics choose useless titles for articles and chapters? Four steps to getting a better title.

An informative title for an article or chapter maximizes the likelihood that your audience correctly remembers enough about your arguments to re-discover what they are looking for. Without embedded cues, your work will sit undisturbed on other scholars’ PDF libraries, or languish unread among hundreds of millions of other documents on the Web.Patrick Dunleavy presents examples of frequently used useless titles and advises on using a full narrative title, one that makes completely clear your argument, conclusions or findings. 


Via Niklaus Grunwald
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Scooped by Nathan Watson-Haigh
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Ten Useful Openstack Swift Features | Adrian Smith's Blog

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Scooped by Nathan Watson-Haigh
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GNU Parallel Tutorial

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Scooped by Nathan Watson-Haigh
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What to do when its all relative: How to analyse relative abundance...

Most measurement processes in molecular bioscience yield information about relative abundances only. This can be a result of sample preparation steps where nucl
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Scooped by Nathan Watson-Haigh
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Six Years After Acquisition, Roche Quietly Shutters 454 - Bio-IT World

Six Years After Acquisition, Roche Quietly Shutters 454 - Bio-IT World | cereal bioinformatics | Scoop.it
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Scooped by Nathan Watson-Haigh
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Efficient SNP Discovery for Crop Genomes through Exome Sequencing

Efficient SNP Discovery for Crop Genomes through Exome Sequencing | cereal bioinformatics | Scoop.it
Discover how custom target enrichment from Roche NimbleGen is enabling plant genomics research

Plant genomes are known for their large genetic content, presenting challenges in whole-genome sequencing and data processing.
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Rescooped by Nathan Watson-Haigh from Plant evolution
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Overly simplistic substitution models obscure green plant phylogeny

Overly simplistic substitution models obscure green plant phylogeny | cereal bioinformatics | Scoop.it

Highlights

 

•Plant phylogeny is incompletely resolved.•Molecular evolution often violates phylogenetic model assumptions.•Improved phylogenetic models are being developed.•Data are quickly becoming unlimited for phylogenetic analysis.

 

Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.


Via Pierre-Marc Delaux
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Scooped by Nathan Watson-Haigh
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Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series

Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series | cereal bioinformatics | Scoop.it
RNA-Seq is emerging as an increasingly important tool in biological research, and it provides the most direct evidence of the relationship between the physiological state and molecular changes in cells.
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Scooped by Nathan Watson-Haigh
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Web Tools for miRNA Analysis

Web Tools for miRNA Analysis | cereal bioinformatics | Scoop.it
An overview of databases and repositories of miRNA sequences and expression, a commentary on miRNA target prediction algorithms, tools for miRNA functional investigation, and online pipelines for the analysis of high throughput experiments.
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Rescooped by Nathan Watson-Haigh from Plant evolution
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Update on the genomics and basic biology of Brachypodium: Trends in Plant Science

The scientific presentations at the First International Brachypodium Conference (abstracts available athttp://www.brachy2013.unimore.it) are evidence of the widespread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution, roots, abiotic and biotic stress, comparative genomics, natural diversity, and cell walls) demonstrates that the Brachypodium research community has achieved a critical mass of tools and has transitioned from resource development to addressing biological questions, particularly those unique to grasses.


Via Pierre-Marc Delaux
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Rescooped by Nathan Watson-Haigh from Plant evolution
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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes : Nature Communications : Nature Publishing Group

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes : Nature Communications : Nature Publishing Group | cereal bioinformatics | Scoop.it

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.


Via Pierre-Marc Delaux
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Biswapriya Biswavas Misra's curator insight, June 4, 7:55 PM

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.

Rescooped by Nathan Watson-Haigh from WHEAT
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How Climate Change Will Affect Our Ancient Relationship With Wheat

How Climate Change Will Affect Our Ancient Relationship With Wheat | cereal bioinformatics | Scoop.it
At a time when the worldwide wheat supply needs to grow, we might not even be able to keep it from diminishing.

Via CIMMYT, Int.
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Rescooped by Nathan Watson-Haigh from The science toolbox
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BWA, SOAP, MAQ, BLAT...OMG Alignment Methods!

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

Scooped by Nathan Watson-Haigh
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International Wheat Genome Sequencing Consortium to Receive €1 million from Bayer CropScience for Physical Map Completion

International Wheat Genome Sequencing Consortium to Receive €1 million from Bayer CropScience for Physical Map Completion | cereal bioinformatics | Scoop.it
The International Wheat Genome Sequencing Consortium ( IWGSC ) announced today that it will receive approximately €1 million (EUR) over the next six months from Bayer CropScience (BCS) to support physical mapping of several wheat chromosomes.
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Scooped by Nathan Watson-Haigh
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Bioinformatics Seminar - Professor Gordon Smyth "Variance models for RNA-seq"

Bioinformatics Seminar - Professor Gordon Smyth "Variance models for RNA-seq" | cereal bioinformatics | Scoop.it
Gordon is well known for his development of the limma Bioconductor package for the analysis of differential gene expression using microarrays. More recently his group has led the way in the develop...
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Rescooped by Nathan Watson-Haigh from Virology and Bioinformatics from Virology.ca
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Genome project fosters bioinformatics education

Genome project fosters bioinformatics education | cereal bioinformatics | Scoop.it

Via Mel Melendrez-Vallard, Chris Upton + helpers
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Scooped by Nathan Watson-Haigh
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MinION™ Access Programme from Oxford Nanopore

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Scooped by Nathan Watson-Haigh
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YOKOFAKUN: GNU parallel for #bioinformatics : my notebook

YOKOFAKUN: GNU parallel for #bioinformatics : my notebook | cereal bioinformatics | Scoop.it
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