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Differentially expressed genes distributed ov... [Int J Biol Sci. 2012] - PubMed - NCBI

Abstract
Release of genetically modified (GM) plants has sparked off intensive debates worldwide partly because of concerns about potential adverse unintended effects of GM plants to the agro system and the safety of foods. In this study, with the aim of revealing the molecular basis for unintended effects of a single site insertion GM Kemingdao (KMD) rice transformed with a synthetic cry1Ab gene, and bridging unintended effects of KMD rice through clues of differentially expressed genes, comparative transcriptome analyses were performed for GM KMD rice and its parent rice of Xiushui11 (XS11). The results showed that 680 differentially expressed transcripts were identified from 30-day old seedlings of GM KMD rice. The absolute majority of these changed expression transcripts dispersed and located over all rice chromosomes, and existed physical distance on chromosome from the insertion site, while only two transcripts were found to be differentially expressed within the 21 genes located within 100 kb up and down-stream of the insertion site. Pathway and biology function analyses further revealed that differentially expressed transcripts of KMD rice were involved in certain biological processes, and mainly implicated in two types of pathways. One type was pathways implicated in plant stress/defense responses, which were considerably in coordination with the reported unintended effects of KMD rice, which were more susceptible to rice diseases compared to its parent rice XS11; the other type was pathways associated with amino acids metabolism. With this clue, new unintended effects for changes in amino acids synthesis of KMD rice leaves were successfully revealed. Such that an actual case was firstly provided for identification of unintended effects in GM plants by comparative transciptome analysis.
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Molecular Techniques in Crop Improvement - genotyping.eu

Molecular Techniques in Crop Improvement - genotyping.eu | Plant Genomics | Scoop.it
Metabolomics: Novel Tool For Studying Complex Biological Systems. 21.Transcriptomic analysis of multiple environmental stresses in plants. D. Transgenic Technologies: 22.Marker-free targeted transformation.
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Reshaping of the maize transcriptome by domestication

[PNAS] Domestication reshaped the maize transcriptome [Plant Biology]: Through domestication, humans have substa...
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Polyketide cyclase from Cannabis sativa [Plant Biology] « Science ...

We analyzed the transcriptome of glandular trichomes from female cannabis flowers, which are the primary site of cannabinoid biosynthesis, and searched for polyketide cyclase-like enzymes that could assist in OA cyclization ...
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Hybrid vigour undressed - leap forward in understanding of the core ...

... of genetic parasites in DNA. Genetic parasites are widespread and it is not surprising that a basic biological ability of plants is self-protection of the plant genome against adverse effects triggered by mobile genetic parasites.
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Czech scientists participate in sequencing banana genome - Prague Daily Monitor

Czech scientists participate in sequencing banana genome - Prague Daily Monitor | Plant Genomics | Scoop.it
DigitalJournal.comCzech scientists participate in sequencing banana genomePrague Daily MonitorPrague, July 16 (CTK) - Czech scientists have participated in the sequencing of the banana genome in which researchers from seven countries took part and...
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BMC Bioinformatics | Full text | Genome plasticity and systems evolution in Streptomyces

Streptomycetes are filamentous soil-dwelling bacteria.
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Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny

Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny | Plant Genomics | Scoop.it

Because of its ancient origin more than 1 billion years ago, the highly reduced plastid genomes of Plantae (e.g., plant chloroplasts) provide limited insights into the initial stages of endosymbiont genome reduction. The photosynthetic amoeba Paulinella provides a more useful model to study this process because its alpha-cyanobacterium–derived plastid originated ∼60 Ma and the genome still contains ∼1,000 genes. Here, we compared and contrasted features associated with genome reduction due to primary endosymbiosis in Paulinella plastids and in marine, free-living strains of the picocyanobacterium, Prochlorococcus. Both types of genomes show gene inactivation, concerted evolution, and contraction of gene families that impact highly conserved single-copy phylogenetic markers in the plastid such as psbA, psbC, and psbD. Our data suggest that these photosystem II genes may provide misleading phylogenetic signal because each of the constituent Plantae lineages has likely undergone a different, independent series of events that led to their reduction to a single copy. This issue is most problematic for resolving basal Plantae relationships when differential plastid gene loss was presumably ongoing, as we observe in Paulinella species. Our work uncovers a key, previously unappreciated aspect of organelle genome reduction and demonstrates “work-in-progress” models such as Paulinella to be critical to gain a fuller understanding of algal and plant genome evolution.

 

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Banana genome sequencing may aid pest-plagued fruit

Banana genome sequencing may aid pest-plagued fruit | Plant Genomics | Scoop.it
Tropical-fruit researchers were breaking out the banana daiquiris Wednesday to celebrate the sequencing of the banana genome by scientists in France.
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Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress. | Shoal.In!

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress. | Shoal.In! | Plant Genomics | Scoop.it
Related Articles Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress. Genet Mol Res.
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Genetic difference between tomato and potato only 8%

Genetic difference between tomato and potato only 8% | Plant Genomics | Scoop.it
There are only about 500 genes specific to tomato," explained Dr Akhilesh Kumar Tyagi, Director, National Institute of Plant Genome Research, one of the three Indian members of the international tomato consortium.
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Proteomic analysis of salicylic acid induced resistance to magnaporthe oryzae in susceptible and resistant rice - Li - PROTEOMICS - Wiley Online Library

Proteomic analysis of salicylic acid induced resistance to magnaporthe oryzae in susceptible and resistant rice - Li - PROTEOMICS - Wiley Online Library | Plant Genomics | Scoop.it
輪読 Proteomic analysis of salicylic acid induced resistance to magnaporthe oryzae in susceptible and resistant rice.
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The Hindu : Sci-Tech / Science : Banana genome sequence will aid crop improvement

The Hindu : Sci-Tech / Science : Banana genome sequence will aid crop improvement | Plant Genomics | Scoop.it
The whola banana genome read.Important for crop quality, productivity and plant health in developing countries http://t.co/yaWoSYwz...
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Transcript profiling reveals complex auxin signalling pathway and ... - 7thSpace Interactive (press release)

Transcript profiling reveals complex auxin signalling pathway and ...7thSpace Interactive (press release)To characterize the molecular events ofthis unique process, transcriptome analysis, in combination with biochemical and histologicalapproaches,...
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Banana genome sequencing gives a boost to pest-plagued fruit

Banana genome sequencing gives a boost to pest-plagued fruit | Plant Genomics | Scoop.it
Breeding a stronger, better banana is not for the weak-willed.
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BMC Genomics | Full text | Mining the Gene Wiki for functional genomic knowledge

Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor.
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Digital Transcriptome Analysis of Putative Sex-Determination Genes in

To identify the candidate genes for sex determination, we conducted a transcriptome analysis of flower samples from male, female and hermaphrodite plants using high-throughput SuperSAGE for digital gene expression ...
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Salt cress genome provides new clues for adaptive evolution

Salt cress genome provides new clues for adaptive evolution | Plant Genomics | Scoop.it
In an article entitled, “Insights into salt tolerance from the genome of Thellungiella salsuginea”, published online in July 9, 2012, issue of PNAS 1-6, the lead author Hua-Jun Wu with thirty five other associates from seven.
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Molecular Techniques in Crop Improvement » nuclease.de

Molecular Techniques in Crop Improvement » nuclease.de | Plant Genomics | Scoop.it
Metabolomics: Novel Tool For Studying Complex Biological Systems. 21.Transcriptomic analysis of multiple environmental stresses in plants. D. Transgenic Technologies: 22.Marker-free targeted transformation.
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Ripe time for tomato genetics - Charlotte Observer

Ripe time for tomato genetics - Charlotte Observer | Plant Genomics | Scoop.it
Ripe time for tomato geneticsCharlotte ObserverRecent research from a North Carolina site of a global plant-development company revealed the tomato has at least 7000 more genes than do humans.
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Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement | Critical Pedagogy

Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement | Critical Pedagogy | Plant Genomics | Scoop.it
Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for...
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Bananas and genetic engineering: Past, present and future - Los Angeles Times

Bananas and genetic engineering: Past, present and future - Los Angeles Times | Plant Genomics | Scoop.it
Bananas and genetic engineering: Past, present and futureLos Angeles TimesAnd the plant starts making antimicrobial chemicals. To name just two examples.
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PLoS ONE: Integrated Metabolo-Proteomic Approach to Decipher the Mechanisms by Which Wheat QTL (Fhb1) Contributes to Resistance against Fusarium graminearum

PLoS ONE: Integrated Metabolo-Proteomic Approach to Decipher the Mechanisms by Which Wheat QTL (Fhb1) Contributes to Resistance against Fusarium graminearum | 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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The evolution of the banana, star of the Western fruit bowl

The evolution of the banana, star of the Western fruit bowl | Plant Genomics | Scoop.it
Did you hear? The genome of the banana has been sequenced, an important development in scientists’ efforts to produce better bananas.
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Plant Cytogenetics: Genome Structure and Chromosome Function (Plant Genetics and Genomics: Crops and Models) e-book downloadsPlant Cytogenetics: Genome Structure and Chromosome Function (Plant G...

Plant Cytogenetics: Genome Structure and Chromosome Function (Plant Genetics and Genomics: Crops and Models) e-book downloadsPlant Cytogenetics: Genome Structure and Chromosome Function (Plant G... | Plant Genomics | Scoop.it
Plant Cytogenetics: Genome Structure and Chromosome Function (Plant Genetics and Genomics: Crops and Models) e-boo http://t.co/XMaMg0yq...
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