Plant Genomics
Follow
Find
10.6K views | +5 today
Plant Genomics
Updates on Plant Genomics
Your new post is loading...
Your new post is loading...
Rescooped by Biswapriya Biswavas Misra from Plant Pathogenomics
Scoop.it!

New Phytologist: Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen (2012)

New Phytologist: Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen (2012) | Plant Genomics | Scoop.it

• Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato.
• We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified.
• A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production.
• Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.


Via Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

How plants make cocaine - Science Codex

How plants make cocaine - Science Codex | Plant Genomics | Scoop.it
Science CodexHow plants make cocaineScience CodexTo find the corresponding enzyme in cocaine biosynthesis, Jan Jirschitzka, a PhD student in the group, searched the genome of the coca plant to look for SDR-like proteins.
more...
No comment yet.
Rescooped by Biswapriya Biswavas Misra from Plant Pathogenomics
Scoop.it!

New Phytologist: Powdery mildew genomes in the crosshairs (2012)

New Phytologist: Powdery mildew genomes in the crosshairs (2012) | Plant Genomics | Scoop.it

Meeting report of 2nd International Powdery Mildew Workshop and 3rd New Phytologist Workshop, in Zu¨ rich, Switzerland, February 2012.


Via Kamoun Lab @ TSL
more...
Kamoun Lab @ TSL's comment, May 30, 2012 9:56 AM
Just storified: Some effector assays are prone to artefacts. Add your thoughts using #effectorassays http://sfy.co/11ZF #storify
Scooped by Biswapriya Biswavas Misra
Scoop.it!

The Mermaid's Tale: Whole genome sequencing, yes or no?

The Mermaid's Tale: Whole genome sequencing, yes or no? | Plant Genomics | Scoop.it
Does it strike anyone else as odd that Science has published an article recommending that everyone have their whole genome sequenced for medical purposes, written by the CEO of a DNA sequencing company?
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

The 1000 Genome: The Revolution in DNA Sequencing and the ...

The 1000 Genome: The Revolution in DNA Sequencing and the ... | Plant Genomics | Scoop.it
Author: Kevin Davies Language: English Publisher: Free Press Publication Date: 24 September 2010 ISBN: 2147483647 Paperback: 229 pages Size: 42mbE-book The.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Consortium Releases Pear Genome Data | GenomeWeb Daily ...

Consortium Releases Pear Genome Data | GenomeWeb Daily ... | Plant Genomics | Scoop.it
Dangshansuli. The assembly, which has been aligned using a genetic map that represents pear's 17 chromosomes, reportedly covers an estimated 97.1 percent of the plant's whole genome. Those involved in the study say ...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Relentless Improvements in Throughput, Read-length and Data Quality Fuel Rapid ... - MarketWatch (press release)

GenomeWebRelentless Improvements in Throughput, Read-length and Data Quality Fuel Rapid ...MarketWatch (press release)The newly released Ion Total RNA-Seq Kit v2, developed by Ambion, permits construction of either small RNA or whole transcriptome...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Nothing in Biology Makes Sense: Making sense of genome reduction

Nothing in Biology Makes Sense: Making sense of genome reduction | Plant Genomics | Scoop.it
During experimental evolution, 80% of the bacterial populations exhibited nearly a 10% reduction in genome size, and many of the gene losses occurred in similar regions of the genome, some even across treatments.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Genome-wide genetic changes during modern breeding of maize

The success of modern maize breeding has been demonstrated by remarkable increases in productivity over the last four decades. However, the underlying genetic changes correlated with these gains remain largely unknown. We report here the sequencing of 278 temperate maize inbred lines from different stages of breeding history, including deep resequencing of 4 lines with known pedigree information. The results show that modern breeding has introduced highly dynamic genetic changes into the maize genome. Artificial selection has affected thousands of targets, including genes and non-genic regions, leading to a reduction in nucleotide diversity and an increase in the proportion of rare alleles. Genetic changes during breeding happen rapidly, with extensive variation (SNPs, indels and copy-number variants (CNVs)) occurring, even within identity-by-descent regions. Our genome-wide assessment of genetic changes during modern maize breeding provides new strategies as well as practical targets for future crop breeding and biotechnology.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Comparative population genomics of maize domestication and improvement

Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution1, 2, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines3. We find evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement. We identify a number of genes with stronger signals of selection than those previously shown to underlie major morphological changes4, 5. Finally, through transcriptome-wide analysis of gene expression, we find evidence both consistent with removal of cis-acting variation during maize domestication and improvement and suggestive of modern breeding having increased dominance in expression while targeting highly expressed genes.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

seriesoftubes 0.9.3.2 : Python Package Index

An extended pipeline for Solexa ChIP-seq data (seriesoftubes 0.9.3.2: An extended pipeline for Solexa ChIP-seq data http://t.co/wdgtNZxp...)...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

The Tomato: Ripe, Juicy and Bursting With Genes

The Tomato: Ripe, Juicy and Bursting With Genes | Plant Genomics | Scoop.it
Plant geneticists who sequenced the tomato’s genome in hope of breeding better specimens found that it has 31,760 genes — about 7,000 more than a person.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Department of Biotechnology Announces A Pathbreaking Research ...

Simultaneously, Indian researchers have taken up analysis of specific genes/gene families related to ripening, nutrition, disease resistance and abiotic stress tolerance based on transcriptome data and comparative genomics.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Analysis of maize shows genes involved in domestication - R & D Magazine

Analysis of maize shows genes involved in domestication - R & D Magazine | Plant Genomics | Scoop.it
Analysis of maize shows genes involved in domesticationR & D MagazineCornell researchers, led by Edward Buckler, a US Department of Agriculture-Agricultural Research Station (USDA-ARS) geneticist in Cornell's Institute for Genomic Diversity and...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Parasitic plants 'steal' genes from their hosts - Science Codex

Parasitic plants 'steal' genes from their hosts - Science Codex | Plant Genomics | Scoop.it
Science CodexParasitic plants 'steal' genes from their hostsScience CodexBy looking at the transcriptome (the transcribed products of switched on genes) they found 49 genes transcribed by the parasite, accounting for 2% of their total...
more...
No comment yet.
Rescooped by Biswapriya Biswavas Misra from Plants and Microbes
Scoop.it!

HHMI-GBMF Investigator: Xinnian Dong, Duke University

HHMI-GBMF Investigator: Xinnian Dong, Duke University | Plant Genomics | Scoop.it

Xinnian Dong chose to study plants in part because she’s uncomfortable with the alternative. She is fascinated by immunology, but the more obvious research models were not a good fit. “I feel squeamish working with animals, so I think plants are perfect,” she says. Thanks to that decision 20 years ago, today she is a pioneer in understanding how plant immunity works and spends her days probing the detailed mechanisms of plant–pathogen defense in her lab at Duke University.

 

Postdoc positions available in Xinnian's lab. Please contact her directly.


Via Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Comparative Genomic Analysis of Soybean Flowering Genes ...

Here, we address this by using a computational approach to examine flowering regulatory genes in the soybean genome in comparison to the most studied model plant, Arabidopsis. For this comparison, a genome-wide ...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

International Consortium Studies Corn Genome | Science Business

International Consortium Studies Corn Genome | Science Business | Plant Genomics | Scoop.it
A collaboration of genetic and agricultural scientists from the U.S., Mexico, France, Kenya, and China conducted a comprehensive analysis of the corn genome.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Agilent Expands HaloPlex Target Enrichment for Ion Torrent and ...

Agilent Expands HaloPlex Target Enrichment for Ion Torrent and ... | Plant Genomics | Scoop.it
A great update to this technology. Now capture up to 5Mb of target sequence for Illumina instruments (e.g MiSeq) and 250Kb target sequence on Ion Torrent.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Pear (Pyruss spp.) Genome Completely Sequenced

Pear (Pyruss spp.) Genome Completely Sequenced | Plant Genomics | Scoop.it
For the first time biologists from the pear genome consortium have completed the sequencing of the pear genome.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

New Products: Illumina's Nextera XT Kits; Agilent's HaloPlex System; Ion ... - GenomeWeb

New Products: Illumina's Nextera XT Kits; Agilent's HaloPlex System; Ion ... - GenomeWeb | Plant Genomics | Scoop.it
New Products: Illumina's Nextera XT Kits; Agilent's HaloPlex System; Ion ...GenomeWebIn addition, it has launched the Ion Total RNA-seq kit v2, which enables construction of either small RNA or whole-transcriptome libraries for sequencing on the PGM...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.

more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

The Phytophactor: Genomic studies confirm the tomato is a fruit. Duh!

The Phytophactor: Genomic studies confirm the tomato is a fruit. Duh! | Plant Genomics | Scoop.it
Really? Genomics confirms that the tomato is a fruit, not a vegetable? No, probably just Gisela's lame attempt at humor. There are a lot of good reasons for genomic research, comparing one genome to another, but it doesn't ...
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

It's Time to Bet on Genomics - Forbes

It's Time to Bet on Genomics - Forbes | Plant Genomics | Scoop.it
GenomeWebIt's Time to Bet on GenomicsForbesThis article is by Ronald W. Davis, director of the Stanford Genome Technology Center and professor of biochemistry and genetics at the Stanford University School of Medicine.
more...
No comment yet.
Scooped by Biswapriya Biswavas Misra
Scoop.it!

DOE Joint Genome Institute in the News: DOE JGI Science ...

DOE Joint Genome Institute in the News: DOE JGI Science ... | Plant Genomics | Scoop.it
DOE JGI Science Highlights: Comparative genomics method to tag novel nitrogen-fixation genes. Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops ...
more...
No comment yet.