Category Archives: Genome

Feb. 6, 2013 A group of international scientists has sequenced the draft genome sequence of the rubber tree Hevea brasiliensis, the major commercial source of natural rubber. The manuscript describing the draft genome is published in BMC Genomics.

Scientists have sequenced the draft genome sequence of the rubber tree Hevea brasiliensis, the major commercial source of natural rubber. Rubber is an indispensible commodity that is used in manufacture worldwide, billions dollar industry. The plant has played a vital role in the world economy since 1876. Currently Asia accounts for about 93% of global supply of rubber.

The manuscript describing the draft genome is published in BMC Genomics. The team identify around 12.7% of the almost 70,000 genes as unique, and outline those associated with rubber biosynthesis, rubber wood formation, disease resistance and allergenicity.

The rubber industry is affected by rubber blight -- a fungal disease -- and natural rubber allergenicity, a global medical concern for those repeatedly exposed to latex-containing products (e.g., gloves).

Ahmad Yamin Rahman and colleagues believe that this draft genome information will accelerate the development of high-yielding natural rubber plants. This will lead to assistance in latex production, wood development, disease resistance and allergenicity.

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Tapping into the rubber plant genome

GSC 14 Talk by Jonathan Coddington - The Global Genome Initiative

By: MediomixMedia

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GSC 14 Talk by Jonathan Coddington - The Global Genome Initiative - Video

Posted at: 02/05/2013 2:53 PM By: The Associated Press

LAS CRUCES, N.M. (AP) - Researchers in New Mexico and South Korea say they have mapped the chile pepper genome, a development that could speed efforts to breed new, improved peppers.

Researchers from New Mexico State University's Chile Pepper Institute and Seoul National University announced Tuesday that they have completed a high-resolution draft of the chile genome.

The genome map signals where genes that underlie certain traits are located. Researchers say the data will provide the tools for how to breed desired traits into pepper plants.

The head of the Chile Pepper Institute, Paul Bosland, says possibilities include plants that would use less water, resist pests and diseases and adapt to climate change.

NMSU researchers plan to use the map to investigate disease resistance to chile wilt, one of the leading problems for growers in New Mexico and abroad.

(Copyright 2013 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.)

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NM, Korean researchers map chile pepper genome

Mitochondrial Genome Assembly based on low coverage 454 data (Vlog #5)
In todays blog I talk about the mitochondrial genome assembly project I work on together with a bachelor student. We take low coverage sequence data with 90k sequences obtained with a 454 GS Junior system (Roche). As the motochondrial genome of the stonefly Pteronarcys princeps is already available, we use it as a reference genome to assemble our Dinocras cephalotes genome. We use the program blast+ to compare the Pteronacrys genome with our 454 reads. With an R script we export hits that match the MTgenome reference, including the phred quality values for each read. The MT reads of D. cephalotes are assembled and edited with Geneious Pro and regions with sequencing, quality problems or low coverage are resequenced with Sanger sequencing. Feel free to comment if you have questions or feedback = ) http://www.luckylion.de http References: Stewart, JB, Beckenbach, AT (2006). Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements. Genome, 49, 815--824.

By: sciencelion

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Mitochondrial Genome Assembly based on low coverage 454 data (Vlog #5) - Video

High Performance Genome Analysis Demo
In this video Dr.-Ing. Matthieu Schapranow from the Hasso Plattner Institut (HPI) showcases you the latest research results about the high performance in-memory genome analysis project. For more information about HANA visit: http://www.saphana.com and for more information about the project visit http://www.epic.uni-potsdam.de

By: saptechnology

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High Performance Genome Analysis Demo - Video

Virology Lecture 2013 #3 - Genomes and genetics
A discussion of the seven different types of viral genome, and the pathway to mRNA, followed by an overview of modern viral genetic analysis.

By: Vincent Racaniello

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Virology Lecture 2013 #3 - Genomes and genetics - Video

Genome Assembly and Gap Closure in Lasergene Genomics Suite
DNASTAR #39;s Matt Keyser shows you how to close gaps in your de novo and reference guided genome assemblies in Lasergene Genomics Suite. To learn more about the steps leading up to the gap closure process, please see our Automated Bacterial Genome Closure and De Novo Genome Assembly webinar videos.

By: DNASTARInc

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Genome Assembly and Gap Closure in Lasergene Genomics Suite - Video

The Joy Genome
Where does genuine joy come from? The Joy Genome is an exciting series based on the New Testament Book of Philippians.

By: Paul Allen

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The Joy Genome - Video

Automating CC #39;s in Shruthi-1 with Genome
Having loads of fun with these automation curves

By: Ashley Elsdon

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Automating CC's in Shruthi-1 with Genome - Video

Public release date: 31-Jan-2013 [ | E-mail | Share ]

Contact: Lynn Yarris lcyarris@lbl.gov 510-486-5375 DOE/Lawrence Berkeley National Laboratory

Future research into the underlying causes of neurological disorders such as autism, epilepsy and schizophrenia, should greatly benefit from a first-of-its-kind atlas of gene-enhancers in the cerebrum (telencephalon). This new atlas, developed by a team led by researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) is a publicly accessible Web-based collection of data that identifies and locates thousands of gene-regulating elements in a region of the brain that is of critical importance for cognition, motor functions and emotion.

"Understanding how the brain develops and functions, and how it malfunctions in neurological disorders, remains one of the most daunting challenges in contemporary science," says Axel Visel, a geneticist with Berkeley Lab's Genomics Division. "We've created a genome-wide digital atlas of gene enhancers in the human brain - the switches that tell genes when and where they need to be switched on or off. This enhancer atlas will enable other scientists to study in more detail how individual genes are regulated during development of the brain, and how genetic mutations may impact human neurological disorders."

Visel is the corresponding author of a paper in the journal Cell that describes this work. The paper is titled "A High-Resolution Enhancer Atlas of the Developing Telencephalon." (See below for a list of co-authors.)

The cerebrum is the most highly developed region of the human brain. It houses the cerebral cortex, the so-called "gray matter" where complex information processing events take place, and the basal ganglia, a brain region that helps control movement throughout the body and is involved in certain types of learning. Many of the genes responsible for development of the cerebrum have been identified but most of the DNA elements responsible for expressing these genes - turning them on/off - have not. This is especially true for gene enhancers, sequences of DNA that act to amplify the expression of a specific gene. Characterizing gene enhancers tends to be difficult because an enhancer does not have to be located directly adjacent to the gene it is enhancing, but can in fact be located hundreds of thousands of DNA basepairs away.

"In addition to acting over long distances and being located upstream, downstream or in introns of protein-coding genes, the sequence features of gene enhancers are poorly understood," Visel says. "However, gene-centric studies have provided strong evidence that gene enhancers are critical for normal embryonic development of the brain and have also linked human diseases to perturbed enhancer sequences."

Visel and an international team of researchers met the challenges of systematic identification and functional characterization of gene enhancers in the cerebrum through a combination of ChIP-seq studies and large-scale histological analyses in transgenic mice, in which the activity patterns of human telencephalon enhancers can be studied. ChIP-seq, which stands for "chromatin immunoprecipitation followed by sequencing," is a technique for genome-wide profiling of proteins that interact with DNA.

This combination of approaches enabled Visel and his colleagues to identify over 4,600 candidate embryonic forebrain enhancers. Furthermore, studying mouse embryos they mapped the activity of 145 of these enhancers at high resolution to define where exactly in the developing brain they drive the expression of their respective target genes. The result is a comprehensive, electronically accessible database for investigating the gene regulatory mechanisms of cerebrum development, and for studying the roles of distant-acting enhancers in neurodevelopmental disorders.

"By mapping hundreds of gene enhancer sequences and defining where exactly in the developing brain they are active, our enhancer atlas provides important information to connect non-coding mutations to actual biological functions," Visel says.

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Genome-wide atlas of gene enhancers in the brain online