bioinformatics and plant genomics
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PacBio Blog: Assessment of Highly Complex Alternative Splicing of Neurexins Performed with SMRT Sequencing

PacBio Blog: Assessment of Highly Complex Alternative Splicing of Neurexins Performed with SMRT Sequencing | bioinformatics and plant genomics | Scoop.it
@PNASNews: Assessment of Highly Complex Alternative Splicing of Neurexins Performed with SMRT Sequencing http://t.co/veGDGmLDp4 @Stanford

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SAT-Assembler – A Scalable and Accurate Targeted Gene Assembly Tool for Next-Generation Sequencing Data | RNA-Seq Blog

SAT-Assembler – A Scalable and Accurate Targeted Gene Assembly Tool for Next-Generation Sequencing Data | RNA-Seq Blog | bioinformatics and plant genomics | Scoop.it
Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality

Via Mel Melendrez-Vallard
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Next Generation Cassava Breeding Project

Next Generation Cassava Breeding Project | bioinformatics and plant genomics | Scoop.it

Why is cassava important?

Cassava (Manihot esculenta), a major staple crop, is the main source of calories for 500 million people across the globe. No other continent depends on cassava to feed as many people as does Africa. Cassava is indispensable to food security in Africa. It is a widely preferred and consumed staple, as well as a hardy crop that can be stored in the ground as a fall-back source of food that can save lives in times of famine. Despite the importance of cassava for food security on the African continent, it has received relatively little research and development attention compared to other staples such as wheat, rice and maize. The key to unlocking the full potential of cassava lies largely in bringing cassava breeding into the 21st century.

Why genomic selection?

Genomic Selection is a new plant breeding method that uses statistical modeling to predict how a plant will perform, before it is field-tested. Novel statistical models and bioinformatics tools, combined with increasingly abundant genomic information, have enabled the deployment of prediction-based breeding methods such as Genomic Selection in crop breeding programs. Giving breeders the ability to select based on predictions rather than observations will result in much improved genetic gains and efficiency.

 

CassavaBase

Access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.


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Alternative splicing - Melissa Moore (U Mass/HHMI)

Overview of the different types of alternative splicing and their proteomic consequences.
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Lecture – Basics of RNA-Seq for Differential Gene Expression | RNA-Seq Blog

Lecture – Basics of RNA-Seq for Differential Gene Expression | RNA-Seq Blog | bioinformatics and plant genomics | Scoop.it
  Date: Tuesday, September 23, 2014, 10:00 am - 12:00 pm Location: 402 Walter Instructor(s):   This lecture will

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Trends in Biotechnology - Does genomic selection have a future in plant breeding?

Summary

Plant breeding largely depends on phenotypic selection in plots and only for some, often disease-resistance-related traits, uses genetic markers. The more recently developed concept of genomic selection, using a black box approach with no need of prior knowledge about the effect or function of individual markers, has also been proposed as a great opportunity for plant breeding. Several empirical and theoretical studies have focused on the possibility to implement this as a novel molecular method across various species. Although we do not question the potential of genomic selection in general, in this Opinion, we emphasize that genomic selection approaches from dairy cattle breeding cannot be easily applied to complex plant breeding.


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Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress | bioinformatics and plant genomics | Scoop.it

Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hATelements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions.

  


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