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Genome Sequencing Projects
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[Oomycete] Phytophthora cinnamomi

[Oomycete] Phytophthora cinnamomi | Genome Sequencing Projects | Scoop.it

Sequencing Plans: The pathogen’s widespread impact on both crops and plants in natural ecosystems worldwide affects the global carbon cycle. For example, forest products sequester roughly 15 percent of the total carbon emissions in the United States. By sequencing the genome of P. cinnamomi, researchers would gain a better understanding of this oomycete and be better equipped to study any changes in plant-pathogen relationships such as those resulting from climate change and the introduction into a region of foreign species.

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[Oomycete] Phytophthora infestans

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement1. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential. 

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[Oomycete] Pythium ultimum

Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species.

The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny   with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable   differential expression of suites of genes under abiotic stress and in the presence   of a host. The predicted proteome includes a large repertoire of proteins involved   in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes   in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved   in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference   in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology   with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique   to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion,   the first report of these in a genome outside the metazoans.

 

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[Diatom] Thalassiosira Pseudonana

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for 20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

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[Oomycete] Albugo candida

A recent genome analysis of the oomycete Hyaloperonospora arabidopsidis suggests that a reduction in the number of genes encoding secreted pathogenicity proteins,   enzymes for assimilation of inorganic nitrogen and sulphur represent a genomic signature   for the evolution of obligate biotrophy. Here, we report a draft reference genome   of a major crop pathogen Albugo candida (another obligate biotrophic oomycete) with an estimated genome of 45.3 Mb. This is   very similar to the genome size of a necrotrophic oomycete Pythium ultimum (43 Mb) but less than half that of H. arabidopsidis (99 Mb). Sequencing of A. candida transcripts from infected host tissue and zoosporangia combined with genome-wide annotation   revealed 15,824 predicted genes. Most of the predicted genes lack significant similarity   with sequences from other oomycetes. Most intriguingly, A. candida appears to have a much smaller repertoire of pathogenicity-related proteins than H. arabidopsidis including genes that encode RXLR effector proteins, CRINKLER-like genes, and elicitins.   Necrosis and Ethylene inducing Peptides were not detected in the genome of A. candida. Putative orthologs of tat-C, a component of the twin arginine translocase system,   were identified from multiple oomycete genera along with proteins containing putative   tat-secretion signal peptides.
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[Oomycete] nine Phytophthora Plant Pathogens

Cambridge, MA and Corvallis, OR, November 15, 2011 – BGI, the world’s largest genomics organization, announced today that it has entered an agreement with Oregon State University to conduct collaborative de novo genome sequencing and transcriptome analysis of nine Phytophthora  plant pathogens. This agreement kicks off a larger collaborative project between BGI and the Phytophthora Genus Sequencing Consortium, to conduct collaborative de novo genome sequencing and transcriptome analysis of all known species of the Phytophthora genus of destructive plant pathogens. All in all, 150 genomes, together with 300 transcriptomes, will eventually be sequenced under this agreement. The consortium agreement was initiated by Oregon State’s incoming Director of the Center for Genome Research and Biocomputing, Brett Tyler, with the support of an Advisory Board of twelve Phytophthora experts from around the world.

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[Oomycete] Phytophthora parasitica

The oomycete Phytophthora parasitica is a very broad host range pathogen that causes destructive diseases of a wide variety of crop plants including tomato, pepper, eggplant, potato, tobacco, cacao, pineapple, passionfruit, safflower, sesame, common bean, banana, citrus, walnut, almond, pistachio, papaya, peach, plum, apricot, apple, macadamia, pear, avocado, guava, pomegranate, a wide variety of nursery and ornamental plants, and forest ecosystems. Some isolates are also effective pathogens of Arabidopsis thaliana and Medicago truncatula. The overall goal of the project is to create a high quality draft sequence of P. parasitica and identify SNPs additional isolates of diverse host range (including several funded by international partners) in order to enable a comparative genomic analysis of genes that determine host range.
They generated a whole genome shotgun assembly from data generated by Illumina sequencing technology. The resulting ~71Mb draft assembly was made public in November of 2011, and the results of genome annotation will be made public in future releases. Questions about the project should be directed to annotation webmaster.

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[Oomycete] Phytophthora sojae & ramorum

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases,  ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.                    

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[Oomycete] Hyaloperonospora arabidopsidis

Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility.  These attributes comprise a genomic signature of evolution toward obligate biotrophy.                    

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[Diatom] Phaeodactylum tricornutum

[Diatom] Phaeodactylum tricornutum | Genome Sequencing Projects | Scoop.it

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

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[Oomycete] Albugo laibachii

[Oomycete] Albugo laibachii | Genome Sequencing Projects | Scoop.it

Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires “effectors” to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the “CHXCs”, by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata.

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[Oomycete] Saprolegnia parasitica

[Oomycete] Saprolegnia parasitica | Genome Sequencing Projects | Scoop.it

The oomycete Saprolegnia parasitica and related pathogens are water molds in the class of Saprolegniomycetidae that attack a wide variety of fish, amphibians and crustaceans important to aquaculture and to aquatic ecosystems. They cause Saprolegniosis, a disease that is characterized by visible white or grey patches of filamentous mycelium on the body or fins of freshwater fish. Saprolegnia parasitica is economically one of the most important fish pathogens, especially on catfish, salmon and trout species. It causes millions of dollar losses to the aquaculture industry worldwide and has also been linked to declining wild fish stocks and amphibian populations around the world.

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[Oomycete] Phytophthora capsici

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually-recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic/genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) and higher levels of single nucleotide variants (SNVs) than those reported for humans, plants, and P. infestans. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 SNV sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

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