Plant Genomics
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PLOS Computational Biology: Interpretation of Genomic Variants Using a Unified Biological Network Approach

PLOS Computational Biology: Interpretation of Genomic Variants Using a Unified Biological Network Approach | Plant Genomics | Scoop.it
PLOS Computational Biology is an open-access
Biswapriya Biswavas Misra's insight:

The decreasing cost of sequencing is leading to a growing repertoire of personal genomes. However, we are lagging behind in understanding the functional consequences of the millions of variants obtained from sequencing. Global system-wide effects of variants in coding genes are particularly poorly understood. It is known that while variants in some genes can lead to diseases, complete disruption of other genes, called ‘loss-of-function tolerant’, is possible with no obvious effect. Here, we build a systems-based classifier to quantitatively estimate the global perturbation caused by deleterious mutations in each gene. We first survey the degree to which gene centrality in various individual networks and a unified ‘Multinet’ correlates with the tolerance to loss-of-function mutations and evolutionary conservation. We find that functionally significant and highly conserved genes tend to be more central in physical protein-protein and regulatory networks. However, this is not the case for metabolic pathways, where the highly central genes have more duplicated copies and are more tolerant to loss-of-function mutations. Integration of three-dimensional protein structures reveals that the correlation with centrality in the protein-protein interaction network is also seen in terms of the number of interaction interfaces used. Finally, combining all the network and evolutionary properties allows us to build a classifier distinguishing functionally essential and loss-of-function tolerant genes with higher accuracy (AUC = 0.91) than any individual property. Application of the classifier to the whole genome shows its strong potential for interpretation of variants involved in Mendelian diseases and in complex disorders probed by genome-wide association studies.

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PLOS ONE: De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids

PLOS ONE: De Novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial Terpenoids | Plant Genomics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Abstract

Herbal remedies are increasingly being recognised in recent years as alternative medicine for a number of diseases including cancer. Curcuma longa L., commonly known as turmeric is used as a culinary spice in India and in many Asian countries has been attributed to lower incidences of gastrointestinal cancers. Curcumin, a secondary metabolite isolated from the rhizomes of this plant has been shown to have significant anticancer properties, in addition to antimalarial and antioxidant effects. We sequenced the transcriptome of the rhizome of the 3 varieties of Curcuma longa L. using Illumina reversible dye terminator sequencing followed by de novo transcriptome assembly. Multiple databases were used to obtain a comprehensive annotation and the transcripts were functionally classified using GO, KOG and PlantCyc. Special emphasis was given for annotating the secondary metabolite pathways and terpenoid biosynthesis pathways. We report for the first time, the presence of transcripts related to biosynthetic pathways of several anti-cancer compounds like taxol, curcumin, and vinblastine in addition to anti-malarial compounds like artemisinin and acridone alkaloids, emphasizing turmeric's importance as a highly potent phytochemical. Our data not only provides molecular signatures for several terpenoids but also a comprehensive molecular resource for facilitating deeper insights into the transcriptome of C. longa.

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Genome Biology | Abstract | Food for thought from plant and animal genomes

A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
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A Solid-State DNA Sequencer Developed by Nabsys Could Reveal the Long-Range Structure of DNA Sequences | MIT Technology Review

A Solid-State DNA Sequencer Developed by Nabsys Could Reveal the Long-Range Structure of DNA Sequences | MIT Technology Review | Plant Genomics | Scoop.it
Nabsys’s technology could provide the positional accuracy missing from current DNA sequencing methods.
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A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP ... - 7thSpace Interactive (press release)

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP ...
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BusinessMirror - Genome sequence of 90 chickpea lines decoded

BusinessMirror - Genome sequence of 90 chickpea lines decoded | Plant Genomics | Scoop.it
The online version of the Philippines' leading business newspaper features virtually all the stories and statistical data available in the print edition.
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No slipping up: Banana proteome unpeeled using peptide libraries - spectroscopyNOW.com

No slipping up: Banana proteome unpeeled using peptide libraries - spectroscopyNOW.com | Plant Genomics | Scoop.it
spectroscopyNOW.com
No slipping up: Banana proteome unpeeled using peptide libraries
spectroscopyNOW.com
There have been a number of studies on the banana to identify metabolites in the fruit but there has been very little proteome activity.
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Analysis of the leaf transcriptome of Musa acuminata during ...

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development - up-to-the-minute news and headlines. 7thSpace is a online portal ...
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iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data - up-to-the-minute news and headlines.
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Transcriptomic analysis of differentially expressed genes during anther ... - 7thSpace Interactive (press release)

Transcriptomic analysis of differentially expressed genes during anther ...
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De novo prediction of the genomic components and capabilities for ...

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes - up-to-the-minute news and headlines. 7thSpace is a online portal covering topics such as ...
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Seed-patent case in Supreme Court - Nature.com

Seed-patent case in Supreme Court - Nature.com | Plant Genomics | Scoop.it
Nature.com
Seed-patent case in Supreme Court
Nature.com
Patents owned by Monsanto required the insertion of three different genes into the plant genome.
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Proteome Science | Abstract | Comparative proteomic analysis of the ...

... omega-gliadins. Detailed proteomic analyses of the effects of fertilizer and high temperature on individual gliadin and glutenin protein levels are needed to determine how these environmental factors influence flour quality.
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A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP ... - 7thSpace Interactive (press release)

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP ...
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PLOS ONE: De Novo Assembly, Gene Annotation and Marker Development Using Illumina Paired-End Transcriptome Sequences in Celery (Apium graveolens L.)

PLOS ONE: De Novo Assembly, Gene Annotation and Marker Development Using Illumina Paired-End Transcriptome Sequences in Celery (Apium graveolens L.) | Plant Genomics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Biswapriya Biswavas Misra's insight:
AbstractBackground

Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding.

Principal Findings

Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp) that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr) and Swiss-Prot database respectively, and 10,473 (24.77%) unigenes were assigned to Clusters of Orthologous Groups (COG). 21,126 (49.97%) unigenes harboring Interpro domains were annotated, in which 15,409 (36.45%) were assigned to Gene Ontology(GO) categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.

Conclusions

This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

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Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling

Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling - up-to-the-minute news and headlines.
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Researchers trace roots of ginkgo tree, cycad plants - Taipei Times

Researchers trace roots of ginkgo tree, cycad plants - Taipei Times | Plant Genomics | Scoop.it
Researchers trace roots of ginkgo tree, cycad plants Taipei Times The team led by Chaw established the largest and most diverse gymnosperm chloroplast genome database to date, including 25 gymnosperm chloroplast genomes with 35,994 nucleotides and...
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Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence - Natural Product Reports (RSC Publishing)

Plant natural product research can be facilitated through genome and transcriptome sequencing approaches that generate informative sequence and expression datasets that enable characterization of biochemical pathways of interest.
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'Zoomable' map of poplar proteins offers new view of bioenergy crop

'Zoomable' map of poplar proteins offers new view of bioenergy crop | Plant Genomics | Scoop.it
Researchers seeking to improve production of ethanol from woody crops have a new resource in the form of an extensive molecular map of poplar tree proteins, published by a team from the U.S. Department of Energy's Oak Ridge National Laboratory.
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Genome sequence of 90 chickpea lines decoded - Business Mirror

Genome sequence of 90 chickpea lines decoded - Business Mirror | Plant Genomics | Scoop.it
Genome sequence of 90 chickpea lines decoded Business Mirror HYDERABAD, India—In a scientific breakthrough that promises improved grain yields and quality, greater drought tolerance and disease resistance, and enhanced genetic diversity, a global...
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Sequencing of the genome of the rubber tree, Hevea brasiliensis | asaislam.org

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Antagonistic, overlapping and distinct responses to biotic stress in rice ... - 7thSpace Interactive (press release)

Antagonistic, overlapping and distinct responses to biotic stress in rice ...
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Transcriptome analysis of developing ovules in rice isolated by laser microdissection

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Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis ... - 7thSpace Interactive (press release)

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis ...
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BetaKit » Bina Launches to Take a Big Data Approach to Genome ...

BetaKit » Bina Launches to Take a Big Data Approach to Genome ... | Plant Genomics | Scoop.it
Big data has been a big trend over the past year, with startups like Platfora and Cloudera helping companies process and make use of their data in real-time. Increasingly solutions are emerging for specific industries or roles, ...
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