MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'genome sequencing'. Sat, 03 Sep 2011 02:29:18 +0100 http://www.medworm.com/index.php?rid=4322636&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FgRRZQti7WfU%2F New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus.  There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place.  The synteny-based evidence was another way to find a phyloge... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4322636 Fri, 07 Jan 2011 19:24:01 +0100 4322636 http://www.medworm.com/index.php?rid=4285301&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FrYtx4OOtgDY%2F Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the general purpose genome biologists with descriptions of next generation/2nd generation sequencing technologies, assembly methods, and comparative genomics. Much more inside these papers than I am summarizing so I urge you to take look if you have access to these pay-for-view articles or contact the authors for reprints to get a copy. These include the genome of biotrophic oomycete and Arabidopsis pathogen Hyaloperonospora arabidopsidis (Baxter et al). Wh... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4285301 Thu, 23 Dec 2010 16:11:50 +0100 4285301 http://www.medworm.com/index.php?rid=3976637&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F79B_MJ5P7io%2F The Broad Institute released their sequence of the genome of Geomyces destructans implicated in the White Nose Syndrome that is causing a massive die-offs of bats. The researchers sequenced a North America isolated strain in this project which is part of an epidemic spreading across the Northeastern United States. This is just the assembly of the genome not the annotation which will be forthcoming. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3976637 Thu, 16 Sep 2010 20:46:56 +0100 3976637 http://www.medworm.com/index.php?rid=3743644&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FqAGH5CCKq5k%2F I am excited to announce the publication of another mushroom genome this week. The mushroom Schizophyllum commune is an important model system for mushroom biology, development of genome was sequenced as part of efforts at the Joint Genome Institute and a collection of international researchers.  The data and analyses from these efforts are presented in a publication appearing in Nature Biotechnology today. Studies in mushrooms can have important impact on other research areas.  They can be useful in biotechnology as protein biosynthesis factories for producing compounds or even as an edible delivery mechanism for new drugs.  What we found in the analysis of this genome include clues to mechanisms of how white rotting fungi degrade lignin through analysis of enzyme families.  We also ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3743644 Mon, 12 Jul 2010 07:12:10 +0100 3743644 http://www.medworm.com/index.php?rid=3710720&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FHmUqNNb51wE%2F I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper. Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D.,... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3710720 Tue, 29 Jun 2010 17:35:11 +0100 3710720 http://www.medworm.com/index.php?rid=3671928&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FQxLvqBv_sO4%2F Francis Martin has written up a delightful summary pointing to our publication of the genome of Coprinopsis cinereus which appears in the early edition of PNAS and will grace the cover at the end of the month.  I encourage you to take a look at Francis’s post and the paper, available as Open Access from PNAS.  I’ll do my best to post a summary of the paper when I get a free moment. For now I’ll leave you with a picture of this cute little mushroom fruting in the lab and a link to many more at Flickr. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3671928 Thu, 17 Jun 2010 21:05:32 +0100 3671928 http://www.medworm.com/index.php?rid=3585767&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FCyx0pBSS2FU%2F Several groups working on Fungi are submitting proposals to the JGI Community Sequencing Program.  Several proposals relating to the JGI’s interest in an encyclopedia of fungal genomes sequencing genomes of ascomycete and basidiomycete yeasts, filamentous ascomycetes, basidiomycetes,  and early diverging fungi are being put forward.  If you haven’t been contacted by these community members but would like to write a letter of support in these areas, please get in touch as the deadline for the proposals in early next week. There are also other proposals going in for Neurospora mutant strain resequencing, more Fusarium species, transcriptomes of mycorrhizal fungi, and other topics.  If you are are a user of data from any of the previous fungal projects that you know how imp... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3585767 Thu, 20 May 2010 20:49:13 +0100 3585767 http://www.medworm.com/index.php?rid=3471972&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FoHra8g2mYaY%2F A couple of papers should have captured your attention lately in the realm of fungal genomics. One is the publication of the genome of the black truffle Tuber melanosporum. This appears as an advanced publication at Nature (OA by virtue of Nature’s agreement on genome papers) along with a NYT writeup and is a tasty exploration of the genome of an ascomycete ectomycorrhizal (ECM) fungus. There are several gems in there including the differences in transposable element content, content of gene families related to carbohydrate metabolism. This genome helps open the doorway for exploring the several independent origins of ECM in both ascomycete and basidiomycete fungi. I’ll also point out there is some work on the analysis of mating type locus found in this genome has applied aspe... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3471972 Thu, 15 Apr 2010 15:03:53 +0100 3471972 http://www.medworm.com/index.php?rid=3172143&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FALk2EqU95xw%2F These papers got lost in my drafts of things to write about.  Grants and overdue manuscripts are keeping me away from the blog. Published work from Gary Foster’s lab in Applied Env Micro show progress on genetic engineering tools to express introduced genes in the basidiomycete mushroom system Clitopilus passeckerianus. C. passeckarianus produces an antibiotic, pleuromutilin, an important antibiotic. Cover photo [Press] They also showed the  5′ intron is important for efficient expression, something that has been shown several times in fungi and provides more evidence for the role of introns in promoting or regulating an aspect of gene expression or translation. Perhaps by splicing-dependent export. Corradi et al – the genome of the microsporidia parasite of Daphn... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3172143 Wed, 13 Jan 2010 00:25:10 +0100 3172143 http://www.medworm.com/index.php?rid=2793358&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2Ft8b-RRiEZtg%2F A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics. In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2793358 Mon, 14 Sep 2009 18:14:35 +0100 2793358 http://www.medworm.com/index.php?rid=2719896&cid=t_114936_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2009%2F08%2Fwhere-from-here.html This is the question I am asked so often.1. We have the steady progress towards cheap genomes. 2. We have the biggest supporter of personalized medicine running the NIH 3. We have "some" clinical awareness of personalized medicine 4. We have the government aware of the shenanigans of some unscrupulous DTC advertising, etc 5. We have several milemarkers under our belts with genome science..... We are moving in the "right" direction, but where do we go from here There are several areas we need to investigate. I would like to sum a few of them, both basic science and clinical. Basic Science first. 1. We need to understand precisely how gene regulation occurs in the face of certain common environmental exposures. Trans Fat, Tobacco Smoke, Alcohol, Stress. Is it RNA? Is it Methylation? What pr... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=2719896 Thu, 20 Aug 2009 14:26:00 +0100 2719896 http://www.medworm.com/index.php?rid=2691703&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F1Rts0G29jXk%2F There is an article in Wine Spectator (Seen on the JGI feed) on sequencing the wine spoilage yeast bruxellensis (correct name is now Dekkera bruxellensis) which adds the not-so-excellent taste of “sweaty horse” to wines.  There is already some survey sequencing done by Ken Wolfe and Jurge Piskur’s groups so a full genome sequencing project will help work out how this yeast is able to out compete Saccharomyces and cause dramatic wine spoilage.  This is also relevant on the bio-fuel side since this yeast can also taint an ethanol bio-reactor.  It is an interesting ecology inside the wine bottle and this competition for resources can lead to bad tasting wine. The competition presumably originated in some form in the rotting fruit where these yeasts compete for space and ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2691703 Tue, 11 Aug 2009 19:17:04 +0100 2691703 http://www.medworm.com/index.php?rid=2571006&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F5rYRQ7HKCbw%2F Tremella mesenterica (from K. Findley) The Tremella mesenterica genome portal is now live at the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes, a significantly larger number of peptides predicted for C. neoformans (~7000; 18Mb genome) which may represent new and interesting genes or aspects of gene loss in the Cryptococcus yeast lineage. Tremella is a Basidiomycete jelly fungus and an interesting study system from the perspective of discovery of novel lignin degrading enzymes.  It also occupies an interesting phylogenetic position being an outgroup to the human pathogenic yeast Cryptococcus neoformans and C. gattii. Comparative genomics on this system may also provide insight into the interesting evolution of the large mating-type locus that was formed throug... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2571006 Thu, 02 Jul 2009 20:43:42 +0100 2571006 http://www.medworm.com/index.php?rid=2512405&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FHEThPiK8Qy0%2F What does mega-search engine Google and mega-genome services company 23andMe have in common? Two actually, and maybe more… First – investments and second, spouses. This week, Google invested $2.6 million in 23andMe on top of the $7 million invested so far. No surprise there, since Google’s co-founder Sergey Bring is the spouse of 23andMe’s co-founder Anne Wojcicki. But as CNN remarked, it’s one the perks of marrying Google.   In another news, biotech giant Illumina has launched a personal genome sequencing service. That is, you can have your entire genome sequenced – all 3 billion DNA - for a hefty price of $48,000. Unlike 23andMe and other genome-testing services where only genotypes are provided, Illumina will provide your entire DNA sequence. But you need a prescr... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=2512405 Sun, 21 Jun 2009 06:58:59 +0100 2512405 http://www.medworm.com/index.php?rid=2274488&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FvBv9bKMjBKQ%2F In preparation for Asilomar, JGI is releasing lots of the genome sequencing project portals. The Schizophyllum commune Genome Portal is now publicly available. Go get your white-rot gene investigation on! (Though please respect the community rules for 1st rights to publication of the genome-wide analyses). © Jason Stajich for The Hyphal Tip, 2009. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Agaricomycota, genome, genome annotation, genome sequencing. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2274488 Mon, 16 Mar 2009 22:55:14 +0100 2274488 http://www.medworm.com/index.php?rid=2260108&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FYGrts5CFiSk%2F Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse. But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing).  The Aspergillus community now has a AGD - Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation. I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of peop... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2260108 Thu, 12 Mar 2009 18:09:35 +0100 2260108 http://www.medworm.com/index.php?rid=2177560&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2009%2F02%2Fntetrasperma-ndiscreta%2F The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work.  These are two closely related species to the well studied laboratory workhorse Neurospora crassa. The N.tetrasperma assembly (8X) has an N50 of 976kb and is highly colinear with the N.crassa genome.  With the JGI, we’ve also done some additional 454 sequencing which will represent an improved assembly and 23X coverage in the next release.  We also did some comparative scaffolding and can basically double that N50 - most of which looks good when compared to the improved V2 assembly. The N.discreta assembly (8X) is also quite good with an N50 of 2.3 Mb. For comparison, the V7 of N.crassa has an N50 ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2177560 Wed, 11 Feb 2009 07:08:50 +0100 2177560 http://www.medworm.com/index.php?rid=2167712&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FCAIJslFGq0M%2F Postia placenta genome is now published in early edition of PNAS.   Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin.  This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author - go Diego!). It is also helpful to contrast the white and brown rotters t... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2167712 Fri, 06 Feb 2009 07:29:42 +0100 2167712 http://www.medworm.com/index.php?rid=2121796&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F519249058%2F The Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.   This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2121796 Thu, 22 Jan 2009 00:42:40 +0100 2121796 http://www.medworm.com/index.php?rid=2027166&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F479999669%2F A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the genome annotation team at the Broad Institute. Some changes noted by the Broad Institute include: “This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process h... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2027166 Tue, 09 Dec 2008 23:18:06 +0100 2027166 http://www.medworm.com/index.php?rid=1984949&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F463183919%2F Genome survey sequencing (1.9X coverage) was generated for Moniliophthora perniciosa, the cause of witches' broom disease on cacao plants. The sequence for this basidiomycete plant pathogen was published in BMC Genomics this week. The authors report a higher number of ROS metabolism and P450 genes. Evaluating whether these copy number differences are significantly different from other basidiomycete fungi and are lineage specific expansions will help determine if these families played a role in the adaptation of this plant pathogen. This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches' broom disease. See related: Will you alway... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1984949 Sun, 23 Nov 2008 21:23:17 +0100 1984949 http://www.medworm.com/index.php?rid=1955292&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2FfWi6LNJnRnQ%2F For the first time, US researchers have decoded all the genes of a woman who died of myeloid leukemia, and they found 10 mutations that contributed to the development of her cancer. This finding is significant on several fronts. It’s the first time that a cancer genome has been sequenced. The scientists took samples of both cancer and normal skin cells from the same woman, and sequenced the DNA on both samples. Previous to this, the focus was on select regions of the genome, called candidate regions, suspected of carrying genes that cause or contribute to cancer. The study also found that 8 of the 10 mutations have never been suspected as contributing to the disease. The researchers found them on every cancer cell and none in the normal samples, which suggests that these mutations ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1955292 Wed, 12 Nov 2008 14:51:03 +0100 1955292 http://www.medworm.com/index.php?rid=1943404&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F445850228%2F From Francis Martin The DNA sequence of Melampsora larici-populina has been determined by the U.S. Department of Energy DOE Joint Genome Institute (DOE JGI). Annotations of the v1.0 assembly of Melampsora laricis-populina are publicly available at http://www.jgi.doe.gov/Melampsora. Genome analyses have been carried out by an international consortium comprised of DOE JGI, France’s National Institute for Agricultural Research (F Martin et al., INRA-Nancy), Canadian Forest Service (R Hamelin et al., Laurentian Forestry Centre), and the Bioinformatics & Evolutionary Genomics Division (Rouzé et al., Gent University) in Belgium. The poplar leaf rust fungus Melampsora is the most devastating and widespread pathogen of poplars, and has limited the use of poplars for environmental and wood ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1943404 Fri, 07 Nov 2008 22:41:53 +0100 1943404 http://www.medworm.com/index.php?rid=1926551&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F438436400%2F Genome Technology highlights the very cool thing about next-gen sequencing - it puts the power in the hands of the researchers to explore genome sequence and doesn't limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke's Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues. This isn't the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has take... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1926551 Fri, 31 Oct 2008 20:56:54 +0100 1926551 http://www.medworm.com/index.php?rid=1844790&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F407728713%2F BBC news and GTO report the sequence of P. chrysogenum, will be published in October in Nat Biotechnology in a project based at the biotech company DSM. P. chrysogenum being the mold that fortuitously contaminated Dr Fleming's bacterial plates. The 13,500 reported genes in the press release is quite bit larger than relatives in the Aspergillus clade (~10,000 genes) so it will be intriguing to see what's going on here and if there will be interesting examples of horizontal transfer like what has been investigated in Aspergillus oryzae. I am unclear as to whether the selected strain is a wild isolate or represents an industrial strain, but look forward to reading the full account of the genome. Factoid - Most of the industrial fungal genome papers have seen publication in Nature Biotechnolog... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1844790 Wed, 01 Oct 2008 20:17:35 +0100 1844790 http://www.medworm.com/index.php?rid=1522208&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F312751464%2F NPR had a story this weekend on Cocoa plantation collapse and the ecological aftermath of the changes the witches' broom fungus Moniliophthora perniciosa has wreaked. The genome sequence project for this Homobasidiomycete fungus (also known as Crinipellis perniciosa, phylogenetic relationships discussed by Aime and Philips-Mora 2005) is underway at the Laboratory Genomica e Expressao at UNICAMP, Brazil.  The witches's broom (not this witches' broom) is named because of the bristly form it induces in the cacao plants. The genome project will hopefully improve the diagnosis and treatment work that is needed.  Beyond the insatiable need for chocolate, the NPR story does talk about the impact on farmers, the economy, and the environment with the loss of these cacao plantations. Some links:... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1522208 Mon, 16 Jun 2008 03:57:26 +0100 1522208 http://www.medworm.com/index.php?rid=1502605&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F307849037%2F (Image credit: medicineworld.org)  This week b5 media’s Health and Wellness channel is focusing on celebrities health.  Our focus is not on ‘tittle tattle’  and hot gossip about Angelina, Brad or ’Tomkat’ but rather a serious look at health issues that high profile individuals share with all of us.  In the genetics world, our ‘celebrities’ are the likes of Craig Venter and James Watson - pioneering geneticists but basking in the eye of the media. The race to sequence genomes has resulted in some major PR, particularly for Craig and James. 454 is sequencing James Watson’s genome and Craig has announced some of his results in PLoS.  TV star Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1502605 Mon, 09 Jun 2008 08:00:52 +0100 1502605 http://www.medworm.com/index.php?rid=1478017&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F300506197%2F At last one for the girls!  … Geneticists at Leiden University Medical Centre (LUMC) are the first to determine the DNA sequence of a woman. She is also the first European whose DNA sequence has been determined The DNA is that of Dutch scientist Dr Marjolein Kriek, a clinical geneticist at LUMC. “If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,”says professor Gert-Jan B van Ommen, leader of the LUMC team.  Now we have  a new ‘Watson and Kriek’ to compare genetic diversity! Elaine Warburton  www.geneticsandhealth.com Tags: DNA, DNA profiling, DNA sequencing, Genome sequencing, Human GenomeShare This (Source: Genetics and Health) Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1478017 Thu, 29 May 2008 11:58:02 +0100 1478017 http://www.medworm.com/index.php?rid=1436934&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F288882594%2F The Trichoderma reesei genome paper was recently published in Nature Biotechnology from Diego Martinez at LANL with collaborators at JGI, LBNL, and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol or other biofuels production.  The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production. The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger numb... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1436934 Mon, 12 May 2008 19:27:46 +0100 1436934 http://www.medworm.com/index.php?rid=1436936&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F288359828%2F The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons among filamentous Sordariomycete fungi. The authors primarily focused on comparative genomics of Podospora to Neurospora crassa, the next closest model filamentous species.  Within the Sordariomycetes there are now a very interesting collection of closely related species which can be useful for applying synteny and phylogenomics approaches. The analyses in the manuscript focused on these differences between Neurospora and Podospora identifying some ke... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1436936 Mon, 12 May 2008 01:25:59 +0100 1436936 http://www.medworm.com/index.php?rid=1429089&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F285930728%2F Neil has a great summary of the results from the Platypus genome sequencing project. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under genome. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1429089 Thu, 08 May 2008 08:07:18 +0100 1429089 http://www.medworm.com/index.php?rid=1426510&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F284944106%2F The transcriptional landscape of yeast has been (further) defined with Solexa sequencing in a method deemed "RNA-Seq", but what I would call "deep EST sequencing".  This approach for transcriptional profiling by sequencing alone is sure to be used by many labs looking for lower and more complete ways to describe and quantitate the full population of transcripts in an organism.   Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. (2008). The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing. Science DOI: 10.1126/science.1158441     © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Br... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1426510 Tue, 06 May 2008 22:25:50 +0100 1426510 http://www.medworm.com/index.php?rid=1419318&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F283191869%2F A nationwide team of researchers, funded in part by the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), has produced the first sequence-based map of large-scale structural variation across the human genome. Recently created maps such as the HapMap have catalogued the patterns of small-scale variations in the genome that involve single DNA letters, or bases.  A sequence-based map provides much finer resolution and location information. Researchers constructed the structural variation map by partially sequencing the genomes of eight people: four people of African descent, two of Asian descent and two of European descent. Sequence data were collected from each end of roughly 1 million random small pieces of DNA from each individual’s ge... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1419318 Sun, 04 May 2008 08:52:50 +0100 1419318 http://www.medworm.com/index.php?rid=1395144&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F276520740%2F Jennifer from the other end of the lab just showed me the Rhizoctonia solani genome project page at JCVI.  Another Basidiomycete genome on the way, yah! © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under basidiomycota, genome sequencing. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1395144 Thu, 24 Apr 2008 00:21:04 +0100 1395144 http://www.medworm.com/index.php?rid=1383715&cid=t_114936_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2008%2F04%2F18%2Fbipolar-genomics%2F Despite much research in recent years, including a study that establishes the heritability of bipolar disorder at 85% (confirming what families and clinicians have known for decades), the precise genetic basis of bipolar disorder remains elusive. Single-gene studies have identified promising candidates here and there, but genome-wide association studies have failed to produce replicable results. Geneticist Dr. Daniel Macarthur recently wrote a super blog post about bipolar gene studies. He explains why several genome-wide association studies involving thousands of patients and controls have not had strong or replicable results. It seems bipolar associations have not been found in variations of the commonly tested genes. Macarthur says that it’s more likely the variations are more r... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=1383715 Sat, 19 Apr 2008 00:04:39 +0100 1383715 http://www.medworm.com/index.php?rid=1349625&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F263534364%2F   (Courtesy of WAMU 88.5 FM American University Radio, Washington, USA) This is a really interesting radio clip from The Diana Rehm Show on WAMU radio on the whole issue of personal genetics. http://wamu.org/programs/dr/08/04/01.php#20091 and click on either the real audio or windows media buttons “A growing number of people are turning to personalized genetic testing to learn about possible predisposition to some diseases, inherited behavioral traits, and clues to their family heritage. We’ll talk about what these tests can tell us and some of the new questions they raise.” Guests Dr. Francis Collins, director of the National Human Genome Research Institute Beth Peshkin, senior genetics counselor, Lombardi Comprehensive Cancer Center, Georgetown University Medical Cen... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1349625 Thu, 03 Apr 2008 19:59:28 +0100 1349625 http://www.medworm.com/index.php?rid=1329090&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F258598373%2F It’s been quite a month for genetics and ethics!  There has been much commentary on GINA (Genetic Information Non discrimination Act) and now an influential academic group have developed an ethical framework of recommendations to encourage individuals to join whole-genome association studies. According to a large group of genomics scholars, researchers, ethicists, and policy designers and watchers, in order to live up to its potential, whole-genome research in the future should be built upon some ETHICAL foundation that will give people the confidence and trust they will need in order to become volunteers. The group of experts published a statement of consensus this week in PLoS Biology that is intended to serve as practical guidance for scientists involved in whole-genome assoc... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1329090 Wed, 26 Mar 2008 22:41:00 +0100 1329090 http://www.medworm.com/index.php?rid=1289304&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F248324387%2F   (Image courtesy of www.ustc.edu.cn)  Latest news from the GenomeWeb: “The Beijing Genomics Institute at Shenzhen announced that it is launching an International Giant Panda Genome Project. Scientists at BGI-Shenzhen plan to sequence a panda to be selected from the Chengdu and Wolong breeding centers using high-throughput sequencing technology. They hope to have a draft genome sequence assembled within six months. The giant panda genome is roughly the same size as the human genome and contains some 20,000 to 30,000 genes. The project is intended to provide new insights into panda ecology and evolution. This could shed light on the panda’s history, migration, and relationships to other animals, as well as information about panda fitness and diseases that may help protect the end... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1289304 Sun, 09 Mar 2008 12:25:35 +0100 1289304 http://www.medworm.com/index.php?rid=1284791&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F247036134%2F Today, I would like to share the news about the publication of the Laccaria bicolor genome. This is the first mycorrhizal symbiotic genome published in the Nature journal. The title is "The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis". The team consisteing of more than 60 researchers from 16 institutions have revealed the interaction between plant and fungi. For complete publication and additional news. © balaji for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under Agaricomycota, basidiomycota, fungi, genome, genome sequencing, symbiosis. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1284791 Thu, 06 Mar 2008 23:11:58 +0100 1284791 http://www.medworm.com/index.php?rid=1277840&cid=t_114936_132_f&fid=35024&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBlindscientist%2F%7E3%2F245598206%2F I’d pay nothing, would never pay a dime to get my genome sequenced. But, Dan Stoicescu is paying US$ 350,000 to get his. He is also retired at the age of 56, and apparently owned Actavis. “I’d rather spend my money on my genome than a Bentley or an airplane,” (…) Mr. Stoicescu said he worried about being seen as self-indulgent (though he donates much more each year to philanthropic causes), egotistical (for obvious reasons) or stupid (the cost of the technology, he knows, is dropping so fast that he would have certainly paid much less by waiting a few months). In my opinion he shouldn’t worry about being seen as a self-indulgent egotistical stupid person. He already is. Whoever drops the philanthropy excuse is a sure winner for the self-indulgent prize, anytime. ... Blind.Scientist blogs http://www.medworm.com/rss/comments.php?id=1277840 Tue, 04 Mar 2008 17:15:35 +0100 1277840 http://www.medworm.com/index.php?rid=1271851&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F244485503%2F The Hebrew University of Jerusalem scientists and others have revealed for the first time the electronic structure of single DNA molecules.  In their work, the researchers were able to decode the electronic structure of DNA and to understand how the electrons distribute into the various parts of the double helix, a result that has been pursued by scientists for many years, but was previously hindered by technical problems. The knowledge that has been acquired in this project may also be relevant for current attempts to develop new sophisticated, reliable, faster and cheaper ways to decode the sequence of human DNA. Finding the electronic structure of DNA was made possible by a collaboration between experimental and theoretical scientists who worked with long and homogeneous DNA molecules ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1271851 Sun, 02 Mar 2008 21:19:49 +0100 1271851 http://www.medworm.com/index.php?rid=1247908&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F238953449%2F David Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanus-S.paradoxus-S.cerevisiae. This updates the Dec 2007 release. (more...) © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under SGRP, genome, genome sequencing, population genomics, resequencing, saccharomyces. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1247908 Thu, 21 Feb 2008 18:50:19 +0100 1247908 http://www.medworm.com/index.php?rid=1230371&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F234590176%2F   First there was Knome at $350,000 per genome sequenced, then HeliScope announced the $70K genome and now Visigen Biotechnologies have announced they have the capability of delivering the holy grail … the $1,000 genome … and by 2010. Have a look at how they propose to achieve this. http://visigenbio.com/technology_movie_streaming.html Visigen Biotechnologies quote: “The technology platform detects the interaction between a fluorescently-tagged polymerase and a fluorescently modified nucleotide. Polymerase is modified with a fluorescent donor molecule and immobilized on a glass slide.  Each nucleotide is color coded with an acceptor fluorescent moiety. During the extension reaction, when a nucleotide is incorporated into the growing polymer, energy transfers from the po... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1230371 Wed, 13 Feb 2008 21:46:14 +0100 1230371 http://www.medworm.com/index.php?rid=1223724&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F233360453%2F The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of 05-Feb-2008. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under bioinformatics, database, fungi, genome, genome annotation, genome sequencing, news. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1223724 Mon, 11 Feb 2008 22:42:37 +0100 1223724 http://www.medworm.com/index.php?rid=1223720&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F233376367%2F    Prostate cancer (Picture courtesy of BBC) UK scientists have found seven new sites in the human genome that are linked to men’s risk of developing prostate cancer.   Dr Ros Eales and Prof Doug Easton  from The Institute of Cancer Research and University of Cambridge respectively, found one gene called MSMB which could possibly be used in screening for prostate cancer and disease monitoring. Another of the sites harbors a gene called LMTK2 which might be a target for new treatments. The data suggests these newly identified genetic alterations are present in over half of all prostate cancer cases. They each increase a person’s risk of the disease by up to 60 per cent. The findings, in summary are: - The five new genetic regions found are on human chromosomes 3, 6, 7, 10, ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1223720 Mon, 11 Feb 2008 21:52:48 +0100 1223720 http://www.medworm.com/index.php?rid=1220688&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F232402204%2F I'm not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences's new sequencing technology that uses detection of DNA polymerase activity to determine sequence.  I believe some of the details are in the paper "Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures", but I've not had a chance to read it. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under conferences, genome sequencing, resequencing. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1220688 Sun, 10 Feb 2008 01:18:23 +0100 1220688 http://www.medworm.com/index.php?rid=1167223&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F220876166%2F The EU funded GEN2PHEN project plans to internationally orchestrate the electronic gathering and use of data that show how gene sequences (’genotypes’) contribute to individual differences in disease, drug response, and other characteristics (’phenotypes’). These relationships (usually in the form of “genotype-phenotype” information stored in scattered databases) are deemed to become essential for future prognosis, diagnosis and treatment of diseases. GEN2PHEN will build a set of database components, tools and technologies that will help all research results pertaining to genome variation and disease to be properly integrated and immediately available for holistic analysis via the internet. The project will deploy a major internet portal, called the &#82... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1167223 Tue, 22 Jan 2008 09:57:30 +0100 1167223 http://www.medworm.com/index.php?rid=1143477&cid=t_114936_131_f&fid=34989&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FGeneticsHealth%2F%7E3%2F214874377%2F Over the last month I have written articles on the rapid advances in genome sequencing (Knowme) and SNP analyses (23andme and deCodeme), all of which are truly awesome.   So when Helicos Biosciences announced it is on track to ship its first next generation sequencing unit called the HeliScope, very soon, it came as no surprise. However …. what blew me away was that they have the capability of sequencing a genome for around $72,000 bringing the $1,000 sequence (considered the ‘Holy Grail’ for sequencing), many steps closer.   HeliScope (TM) Single Molecule Sequencer Helicos President and COO Steve Lombardi  announced at the JPMorgan Healthcare Conference that the HeliScope can do whole-genome sequencing at 10x coverage in eight weeks at a cost of $72,000. He also ... Genetics and Health blogs http://www.medworm.com/rss/comments.php?id=1143477 Fri, 11 Jan 2008 09:20:25 +0100 1143477 http://www.medworm.com/index.php?rid=1106258&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F203015265%2F I've paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project. The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite a bit better than what was there before, but doesn't have a correct treatment of transposons. You can get the data by starting here: http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/datadoc.shtml There is also a new version of the browser: http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/browser.shtml There are a few new features in the browser which [David] is going to document over the next couple of days. Major new features of the data are that there shou... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1106258 Wed, 19 Dec 2007 22:57:46 +0100 1106258 http://www.medworm.com/index.php?rid=1034656&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F186504022%2F The JGI have released the genome sequence and annotation of the Mycosphaerella fijiensis fungus an important crop pathogen of bananas. This Dothideomycete fungus is one of several in the clade of important plant pathogens that have been sequenced recently including M. gramicola, a relative that causes wheat-blotch. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under dothideomycetes, genome. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1034656 Sun, 18 Nov 2007 04:10:19 +0100 1034656 http://www.medworm.com/index.php?rid=956126&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F170818207%2F I also heard through the grapevine that the Mucor ircinelloides genome 4X assembly was completed by JGI and a BLAST server is available if you contact the authors. Mucorales (previously Zygomycota which is not monophyletic) includes previously sequenced Rhizopus oryzae and Phycomyces blakesleeanus which we've blogged about before. Mucor is model system © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under genome sequencing, zygomycete. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=956126 Tue, 16 Oct 2007 20:57:51 +0100 956126 http://www.medworm.com/index.php?rid=956127&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F170811967%2F Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers. "If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project." © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=956127 Tue, 16 Oct 2007 20:41:14 +0100 956127 http://www.medworm.com/index.php?rid=931165&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F165833488%2F Few organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise. What is curious is the large number of yeast genes for which we've been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can't figure this out in yeast, what hope do we have in non-model organisms? Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics. The authors point out several interesting things about these genes of unknown functi... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=931165 Fri, 05 Oct 2007 20:47:03 +0100 931165 http://www.medworm.com/index.php?rid=928808&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F165538880%2F Nature has an overview of what goes in and out of next generation sequencers with an interview with a smiling Chad Nusbaum from the Broad Institute. Most of these have been out and about for a while, but it seems that the hayride/bandwagon is starting to pick up more steam as GT's Genome Scan has several posts about sequencing referencing J. Craig V, George Church, and the Nature news article (not free). Note that Solexa is no longer the cool name - "Genome analyzer" being the name for the machine that was previously called Solexa 1G. I'm holding out hope for funnier names in the future. I do feel that ABI's choice of SOLiD is more exciting than 310/3700/3730 that is as inspiring as HAL9000. But I mean if your technology is called pyrosequencing, I am hoping Roche will come up with a firey... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=928808 Fri, 05 Oct 2007 04:42:56 +0100 928808 http://www.medworm.com/index.php?rid=915411&cid=t_114936_131_f&fid=35743&url=http%3A%2F%2Fthegenesherpa.blogspot.com%2F2007%2F09%2Fabout-helix-health.html Well, I have been getting alot of questions regarding our personalized medical practice on Park Avenue in New York City. I have been reluctant to tell everyone, but I figure that I might as well let everyone in on our "secret"My philosophy is the power of genomics should empower patients and providers. Together as a team we can prevent some horrible diseases and avoid some horrible adverse drug reactions. How do we do this? We take the skills from a multidisciplinary team and identify risk. We feel that the most powerful genomic tool out there is family history (Sorry Hsien). This has been validated over and over again in epidemiological studies. In fact when Mike Leavitt indicate in his foreward of his Personalized Health Care report"One part of the foundation for such a change is our rap... Gene Sherpas: Personalized Medicine and You blogs http://www.medworm.com/rss/comments.php?id=915411 Sun, 30 Sep 2007 23:03:00 +0100 915411 http://www.medworm.com/index.php?rid=873756&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F09%2Ffusarium-graminearum-genome-published%2F The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled "The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion". The project was a collaboration of many different Fusarium research groups. The genome sequencing was spearheaded by the Broad Institute at Harvard and MIT and is part of a larger project to sequence several different species of Fusarium. The group sequenced a second strain in order to identify polymorphisms. Some of the key findings The presence of Repeat Induced point-mutation (RIP) has likely limited the amount of repetitive and duplicated sequences in the genome Most of the genes unique to F. graminearum (and thus not present in 4 other Fusarium spp gen... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=873756 Wed, 12 Sep 2007 06:16:39 +0100 873756 http://www.medworm.com/index.php?rid=714765&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F130543049%2F Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes The Dothideomycete leaf streak disease causing fungus Mycosphaerella fijiensis Soybean rust Phakopsora pachyrhizi The Basidiomycete and jelly fungus Tremella mesenterica proposed by Joe Heitman for use as outgroup to the human pathogen Cryptococcus The plant pathogen Cochliobolus heterostrophus proposed by Gillian Turgeon which ironically was already sequenced at the now closed Syngenta Torrey Mesa Research Institute (i.e. this paper on NRPS which used the genome) The Sordariale Thielavia terrestris proposed by Novoenzymes presumably for potential in producing novel cellulases as part of biofuel production research. The Sordariale and Chestnut blight fungus Cryphonectria pa... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=714765 Wed, 04 Jul 2007 20:00:25 +0100 714765 http://www.medworm.com/index.php?rid=676072&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F124249170%2F The JGI has released the genome sequence and annotation of the Basidiomycete brown rot Postia placenta. Brown rotters can only break down cellulose but do not degrade lignin that white rotters (like Phanerochaete chrysosporium). Using total genomic DNA from dikaryotic strain MAD-698, the JGI generated 571,000 reads that assembled into 1243 haplotype scaffolds, with 85 of these scaffolds covering half of the genome sequence. v.1.0 (September 2006): Postia placenta genome assembly v1.0. The assembly release of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.23X. After trimming for vector and quality, 574,631 reads assembled into 1243 scaffolds totaling 90.9 Mbp. Since Postia placenta is known to be highly polymorph... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=676072 Tue, 12 Jun 2007 16:59:34 +0100 676072 http://www.medworm.com/index.php?rid=566553&cid=t_114936_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F04%2Fmore-neurospora-genomes%2F We got word last week from the JGI that our DNA for Neurospora tetrasperma and N. discreta have passed QC and library QC and are on their way to being sequenced. The center also plans to do some EST sequencing to improve gene calling abilities. Why more Neurospora genomes? The sequencing proposal discussed these species as a model system for evolutionary and ecological genetics. It will allow us and others to test several hypotheses about the molecular evolution of things like genome defense in Neurospora and to understand more about the evolutionary history of the model organism N. crassa. (more…) genome, genome sequencing, neurospora © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking th... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=566553 Tue, 24 Apr 2007 17:54:58 +0100 566553