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Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data.

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data.

Copy number variation (CNV) is believed to actively contribute to adaptive evolution of plant species. While many computational algorithms can be found to detect copy number variation from complete genome sequencing datasets, the everyday complexity of plant knowledge possible introduces false constructive calls.To allow dependable and complete detection of CNV in plant genomes, we developed …

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data. Read More »

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites.

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites.

Most protein-encoding genes in eukaryotes comprise introns, that are interwoven with exons. Introns must be faraway from preliminary transcripts as a way to generate the ultimate messenger RNA (mRNA), which could be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice websites. However, there …

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. Read More »

Bridging genomics and field research: draft genome sequence of Bacillus thuringiensis CR71, an endophytic bacterium that promotes plant growth and fruit yield in Cucumis sativus L.

Bridging genomics and field research: draft genome sequence of Bacillus thuringiensis CR71, an endophytic bacterium that promotes plant growth and fruit yield in Cucumis sativus L.

Here we report the draft genome sequence of bacterial pressure CR71, consisting of a single chromosome with 5,914,775 base pairs (bp), 34.7% G + C content material, and 5733 protein-coding genes. Phylogenetic evaluation signifies that the CR71 pressure is affiliated with┬áBacillus thuringiensis┬áspecies, with an common nucleotide identification > 96% and genome to genome distance > …

Bridging genomics and field research: draft genome sequence of Bacillus thuringiensis CR71, an endophytic bacterium that promotes plant growth and fruit yield in Cucumis sativus L. Read More »

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing.

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing.

Long non-coding RNAs (lncRNAs) play essential roles in regulating gene expression in response to plant stresses. Given the significance regulatory roles of lncRNAs, offering strategies for predicting the perform of these molecules, particularly in non-model crops, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera (Pistacia vera L.) …

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing. Read More »

Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality

Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality

Since sugarcane is a ratoon crop, genome evaluation of plant growth-promoting bacteria that exist in its soil rhizosphere, can present alternative to better perceive their traits and use of such bacteria in flip, might particularly enhance perennial crop productiveness. In the current examine, genome of two bacterial strains, one every of B. megaterium (BM89) and …

Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality Read More »

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant Somatic Embryogenesis Transdifferentiation in Cotton.

As a notable illustration of totipotency and plant regeneration, somatic embryogenesis (SE) is the developmental reprogramming of somatic cells toward the embryogenesis pathway, the key step for genetic engineering. Investigations examining the totipotency process are of great fundamental and practical importance in crop biotechnology. However, high-frequency regeneration of cotton via SE has been limited due to genotype-dependent …

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant Somatic Embryogenesis Transdifferentiation in Cotton. Read More »

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eXtreme Array Mapping Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana David J. Wolyn, Justin O. Borevitz, Olivier Loudet, Chris Schwartz, Julin Maloof, Joseph R. Ecker, Charles C. Berry and Joanne Chory Supplementary Data Kas X Col improved genetic map with additional marker data And .cel files from …

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Methods

RO1 GM073822 Principal Investigator Program Director: Borevitz, Justin GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA Project Description Our proposal will investigate the genetic and molecular basis of complex traits and their interactions with the environment using the model plant Arabidopsis thaliana. We will implement a multi use, high density oligo-nucleotide tiling array for whole genome …

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