Category Archives: Genome

A team of international researchers has sequenced the genome of the Nevada dampwood termite, providing an inside look into the biology of the social insect and uncovering new genetic targets for pest control.

Michael Scharf, a Purdue University professor of entomology who participated in the collaborative study, said the genome could help researchers develop control strategies that are more specific than the broad-spectrum chemicals conventionally used to treat termite infestations.

"The termite genome reveals many unique genetic targets that can be disrupted for better termite control," said Scharf, who is the O. Wayne Rollins/Orkin Chair in Molecular Physiology and Urban Entomology. "Depending on which gene or protein that is targeted, we could disrupt termites' neurological processes, molting, digestive factors or cuticle formation. We're just limited by our imagination."

The Nevada dampwood termite is the first termite species to have its genome sequenced. While dampwood termites do not cause significant damage to buildings, they are closely related to key pests such as the eastern subterranean termite, which is the main pest species in Indiana and the Eastern U.S.

Termites are major pests of human structures, costing an estimated $40 billion in damage and control treatment each year. Having the genome in hand will enable researchers to look for common features expressed across termite species to find control targets effective for all types of termites, Scharf said.

Current termite control measures consist largely of synthetic chemical-based products, some of which are toxic to vertebrates.

"While current pesticides are very effective products, the problem is that you're injecting large volumes of them into the soil around the house," Scharf said. "It would be nice to move to a greener technology, and that's what the genome sequence could enable us to do."

Baiting termites with small quantities of treated wood that they could eat and share with colony-mates would be one such technique, he said. Newer technology such as gene silencing, which targets termite RNA to reduce the expression of critical genes, could also knock out the pests.

"With termites, you don't have to impact all of them," he said. "Targeting just a fraction of the workers could cause an entire colony to collapse."

The study also highlights genes related to chemical communication, the way in which termites "talk" to one another to signal aggression or a desire to reproduce.

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Termite genome lays roadmap for 'greener' control measures

PUBLIC RELEASE DATE:

20-May-2014

Contact: Mick Kulikowski mick_kulikowski@ncsu.edu 919-515-8387 North Carolina State University

North Carolina State University entomologists are part of a research team that has for the first time sequenced the genome of a member of the termite order, the dampwood termite (Zootermopsis nevadensis). A paper reports the findings today in Nature Communications.

The findings on the genetic blueprint of the dampwood termite, one of the world's most primitive social insects, highlight key differences and similarities with other social insects like ants, wasps and bees, and provide insight into how social insects evolved. The findings could also help researchers pinpoint specific gene functions to devise measures to control unwanted termites.

Dampwood termites don't get out much; most of their lives are spent inside a tree log. So it stands to reason that termite males have expanded male fertility genes to continually fertilize eggs produced by queens that don't store sperm for very long. In contrast, ant males deliver sperm once in a short-lived and often far-flung existence, forcing ant queens to store sperm for a long time, says Dr. Ed Vargo, professor of entomology and a co-author of the paper.

"Generally, ant males deliver sperm and then die. But sperm production goes on for life in the dampwood termite male," Vargo said.

The study also shows that termites have fewer receptors associated with smell than other social insects. While this makes sense at a basic level a termite that doesn't leave home may not experience a wide variety of smells and thus has no need for a wide odor palate the finding is also a bit surprising. Dr. R. Michael Roe, an NC State professor of entomology and co-author of the paper, says that previous studies in ants and bees suggest that a sophisticated chemical communication behavior system needs lots of sensory receptor genes.

"These sensory receptors may not be as important to being social as we previously believed, at least for these more primitive termites," Roe said. "These findings also show that you can't make assumptions about termites by studying ants it's important to study both as comprehensively as possible."

The study also found some key similarities between dampwood termites and other social insects. Many of the termite genes involved in sex and caste determination appear to be present in ants, for example.

Continued here:
Researchers sequence genome of primitive termite

After Effects Template Genome Logo Ident
Genome Logo Ident download: http://bit.ly/1nPENqn Cascading effect is always popular, its usually created with professional 3d application like Cinema 4D, 3d...

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Rearrangement Hotspots in the Human Genome
Are There Fragile Regions in the Human Genome? (Part 8/9)

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Rearrangement Hotspots in the Human Genome - Video

VGTV morning newscast - May 20, 2014

10:35 a.m. EDT, May 19, 2014

RICHMOND - The Virginia Department of Forestry announced Monday that a team of scientists from across the nation has decoded the genome of a Virginia Loblolly pine tree.

With 22 billion base pairs, this is the largest genome ever sequenced. In comparison, the human genome has 3 billion base pairs.

Led by Dr. David Neale, professor of plant sciences at the University of California-Davis, the team used tissue from a single pine seedling obtained from the Virginia Department of Foresry and broke down the trees DNA into smaller, more manageable data pieces and analyzed them with a super-computer.

The team then re-assembled the pieces, figured out which genes were present, where they are on the genome, and what they do. This new approach, developed at the University of Maryland, enabled researchers to perform such a large and complex genome sequencing.

Its a huge genome, Neale said in a press release. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order. The contribution of a loblolly pine tree was critically important, not only for the genome sequencing but moreso for all those who follow and will now have completely open access to data and germplasm resources.

The Loblolly pine, grown in the orchard at the Forestry Department's New Kent Forestry Center, was selected for sequencing because of its broad distribution, economic value and long history of genetic research.

Jerre Creighton, VDOFs research program coordinator, said Loblolly pine is the most common tree species in Virginia and the most commercially important tree in the United States. Its the primary source of pulpwood (used to make paper) and sawtimber (lumber). Today, Loblolly pine is being developed as a potential feedstock for the emerging biofuel industry.

The results of this research is expected to help scientists breed improved varieties of Loblolly pines, some of which will be more resistant to pathogens, such as fusiform rust the most damaging disease of southern pines.

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Scientists use Loblolly pine from New Kent to sequence largest genetic code yet

RICHMOND - The Virginia Department of Forestry announced Monday that a team of scientists from across the nation has decoded the genome of a Virginia Loblolly pine tree.

With 22 billion base pairs, this is the largest genome ever sequenced. In comparison, the human genome has 3 billion base pairs.

Led by Dr. David Neale, professor of plant sciences at the University of California-Davis, the team used tissue from a single pine seedling obtained from the Virginia Department of Foresry and broke down the trees DNA into smaller, more manageable data pieces and analyzed them with a super-computer.

The team then re-assembled the pieces, figured out which genes were present, where they are on the genome, and what they do. This new approach, developed at the University of Maryland, enabled researchers to perform such a large and complex genome sequencing.

Its a huge genome, Neale said in a press release. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order. The contribution of a loblolly pine tree was critically important, not only for the genome sequencing but moreso for all those who follow and will now have completely open access to data and germplasm resources.

The Loblolly pine, grown in the orchard at the Forestry Department's New Kent Forestry Center, was selected for sequencing because of its broad distribution, economic value and long history of genetic research.

Original post:
Scientists use Loblolly pine seedling from New Kent to unlock largest genetic code ever sequenced

PUBLIC RELEASE DATE:

19-May-2014

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

Shenzhen, May 18, 2014---Chinese scientists from Chinese Academy of Agricultural Sciences and BGI successfully deciphered the genome sequence of another diploid cotton-- Gossypium arboreum (AA) after the completed sequencing of G. raimondii (DD) in 2012. G. arboreum, a cultivated cotton, is a putative contributor for the A subgenome of cotton. Its completed genome will play a vital contribution to the future molecular breeding and genetic improvement of cotton and its close relatives. The latest study today was published online in Nature Genetics.

As one of the most important economic crops in the world, cotton also serves as an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis. However, breeders and geneticists remain little knowledge on the genetic mechanisms underlying its complex allotetraploid nature of the cotton genome (AADD). It has been proposed that all diploid cotton species present may have evolved from a common ancestor, and all tetraploid cotton species came from interspecific hybridization between the cultivated species G. arboreum and the non-cultivated species G. raimondii.

After the completed sequencing of G. raimondii in 2012, researchers started the work on decoding the genome of G. arboreum. In this study, they sequenced and assembled the G. arboreum genome using whole-genome shotgun approach, yielding a draft cotton genome with the size of 1,694 Mb. About 90.4% of the G. arboretum assembled scaffolds were anchored and oriented on 13 pseudochromosomes.

Furthermore, researchers found the long terminal repeat (LTR) retrotransposons insertions and expansions of LTR families contributed significantly to forming the double-sized G. arboreum genome relative to that of G. raimondii. Further molecular phylogenetic analyses suggested that G. arboreum and G. raimondii diverged about 5 million years ago, and the protein-coding capacities of these two species remained largely unchanged.

To investigate the plant morphology mechanisms of cotton species, a series of comparative transcriptome studies were performed. Results suggested that NBS-encoding subfamilies played an essential role on the immune to Verticillium dahliae. The resistance of G. raimondii on Verticillium dahliae was caused by expansion and contraction in the numbers of NBS-encoding genes, accordingly the loss in the genome of G. arboreum was responsible to their susceptible.

Another interesting finding of this study is the cotton fiber cell growth, and they found the 1-aminocyclo-propane-1-carboxylic acid oxidase (ACO) gene was a key modulator. Researchers suggest the overproduction of ACO maybe the reason why G. raimondii have a poor production of spinnable fiber, while the inactivation of ACO in G. arboreum might benefit its fiber development.

The G. arboreum genome will be an essential reference for the assembly of tetraploid cotton genomes and for evolutionary studies of Gossypium species. It also provides an essential tool for the identification, isolation and manipulation of important cotton genes conferring agronomic traits for molecular breeding and genetic improvement.

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Chinese scientists crack the genome of another diploid cotton Gossypium arboreum

Dr. Warren Kaplan from the Garvan Institute discusses their new HiSeq X Ten powered genome factory.
The Garvan Institute #39;s (@GarvanInstitute) Chief of Informatics, Dr. Warren Kaplan shares lessons learned from the frontlines. At the Illumina Scientific Sum...

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Dr. Warren Kaplan from the Garvan Institute discusses their new HiSeq X Ten powered genome factory. - Video

STi Genome Gauges
Oil Temp 60mm Oil Pressure 60mm Boost 52mm.

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STi Genome Gauges - Video

CRISPR/Cas System from OriGene, a Complete Solution for Targeted Genome Modification
The CRISPR/Cas system is an RNA-guided nuclease system for targeted genomic modification. Due to its amazing simplicity, CRIPSR-based genome editing can be achieved with a simple transfection....

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CRISPR/Cas System from OriGene, a Complete Solution for Targeted Genome Modification - Video