Genomics and metagenomics of microbes
7.5K views | +1 today
Genomics and metagenomics of microbes
Research related to fungal pathogen biology.
Your new post is loading...
Your new post is loading...
Scooped by Bradford Condon
Scoop.it!

Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets

Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets | Genomics and metagenomics of microbes | Scoop.it
A collective animal behavior-inspired algorithm for clustering outperforms traditional clustering algorithms.  Calling gene clusters "flocks" of orthologs is fun.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Frontiers | In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design | Statistical Genetics and Me...

Frontiers | In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design | Statistical Genetics and Me... | Genomics and metagenomics of microbes | Scoop.it
In the past five years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN. Both TMM and DESeq2 are widely used for differential gene expression analysis. This paper introduces properties that show when these three methods will give exactly the same results. These properties are proven mathematically and illustrated by performing in silico calculations on a given RNA-Seq data set.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Exploring the virome of diseased horses

Exploring the virome of diseased horses | Genomics and metagenomics of microbes | Scoop.it
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C viru
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi | Genomics and metagenomics of microbes | Scoop.it
Ropars et al. report newly discovered horizontally transferred regions, flanked by
specific transposable elements that allow cheese-making fungi and food spoilers to
grow faster and be better competitors on cheese. These findings have industrial and
food safety implications and also improve our understanding of adaptation processes.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Basidiomycete yeasts in the cortex of ascomycete macrolichens

Basidiomycete yeasts in the cortex of ascomycete macrolichens | Genomics and metagenomics of microbes | Scoop.it
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure | Genomics and metagenomics of microbes | Scoop.it

Abstract background:

The increasing awareness of the role of phyllosphere microbial communities in plant health calls for a greater understanding of their structure and dynamics in natural ecosystems. Since most knowledge of tree phyllosphere bacterial communities has been gathered in tropical forests, our goal was to characterize the community structure and assembly dynamics of phyllosphere epiphytic bacterial communities in temperate forests in Quebec, Canada. We targeted five dominant tree species: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea, and Picea glauca. We collected 180 samples of phyllosphere communities on these species at four natural forest sites, three times during the growing season.


more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract

Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract | Genomics and metagenomics of microbes | Scoop.it
Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogues, several microbial lineages remain underrepresented. Here we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using Canopy Clustering complemented by visualisation and human-augmented binning using VizBin post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VizBin de novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualisations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Plan to synthesize human genome triggers a mixed response

Plan to synthesize human genome triggers a mixed response | Genomics and metagenomics of microbes | Scoop.it
Some of HGP-write’s proponents have financial stakes in those firms, which include Gen9 in Cambridge, Massachusetts.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

“Human Genome Project-Write” Unveiled | The Scientist Magazine®

“Human Genome Project-Write” Unveiled | The Scientist Magazine® | Genomics and metagenomics of microbes | Scoop.it

An exciting proposal that may or may not be a waste of resources.  I'll be curating more on this as it appears in the news and reserving my own judgements for now.


"The initiative could take 10 years and a minimum of $100 million just to get started..."

more...
No comment yet.
Rescooped by Bradford Condon from Plants and Microbes
Scoop.it!

Nature News: Devastating wheat fungus appears in Asia for first time (2016)

Nature News: Devastating wheat fungus appears in Asia for first time (2016) | Genomics and metagenomics of microbes | Scoop.it

Fields are ablaze in Bangladesh, as farmers struggle to contain Asia’s first outbreak of a fungal disease that periodically devastates crops in South America. Plant pathologists warn that wheat blast could spread to other parts of south and southeast Asia, and are hurrying to trace its origins.

 

Efforts are also under way to find wheat genes that confer resistance to the disease.

 

First detected in February and confirmed with genome sequencing by Kamoun’s lab this month, the wheat-blast outbreak has already caused the loss of more than 15,000 hectares of crops in Bangladesh. “It’s really an explosive, devastating disease,” says plant pathologist Barbara Valent of Kansas State University in Manhattan, Kansas. “It’s really critical that it be controlled in Bangladesh.”

 

After rice, wheat is the second most cultivated grain in Bangladesh, which has a population of 156 million people. More broadly, inhabitants of south Asia grow 135 million tonnes of wheat each year.

 

Wheat blast is caused by the fungus Magnaporthe oryzae. Since 1985, when scientists discovered it in Brazil’s Paraná state, the disease has raced across South America.

 

The fungus is better known as a pathogen of rice. But unlike in rice, where M. oryzae attacks the leaves, the fungus strikes the heads of wheat, which are difficult for fungicides to reach. A 2009 outbreak in wheat cost Brazil one-third of that year’s crop. “There are regions in South America where they don’t grow wheat because of the disease,” Valent says. Wheat blast was spotted in Kentucky in 2011, but vigorous surveillance helped to stop it spreading in the United States.

 

In South America, the disease tends to take hold in hot and humid spells. Such conditions are present in Bangladesh, and the disease could migrate across south and southeast Asia, say plant pathologists. In particular, itcould spread over the Indo-Gangetic Plain through Bangladesh, northern India and eastern Pakistan, warn scientists at the Bangladesh Agricultural Research Institute (BARI) in Nashipur.

 

Bangladeshi officials are burning government-owned wheat fields to contain the fungus, and telling farmers not to sow seeds from infected plots. The BARI hopes to identify wheat varieties that are more tolerant of the fungus and agricultural practices that can keep it at bay, such as crop rotation and seed treatment.

 

It is unknown how wheat blast got to Bangladesh. One possibility is that a wheat-infecting strain was brought in from South America, says Nick Talbot, a plant pathologist at the University of Exeter, UK. Another is that an M. oryzae strain that infects south Asian grasses somehow jumped to wheat, perhaps triggered by an environmental shift: that is what happened in Kentucky, when a rye-grass strain infected wheat.

 

To tackle the question, this month Kamoun’s lab sequenced a fungus sample from Bangladesh. The strain seems to be related to those that infect wheat in South America, says Kamoun, but data from other wheat-infecting strains and strains that plague other grasses are needed to pinpoint the outbreak’s origins conclusively.

 

The Open Wheat Blast website might help. Kamoun has uploaded the Bangladeshi data, and Talbot has deposited M. oryzae sequences from wheat in Brazil. Talbot hopes that widely accessible genome data could help to combat the outbreak. Researchers could use them to screen seeds for infection or identify wild grasses that can transmit the fungus to wheat fields.

 

Rapid data sharing is becoming more common in health emergencies, such as the outbreak of Zika virus in the Americas. Kamoun and Talbot say that their field should follow suit. “The plant-pathology community has a responsibility to allow data to be used to combat diseases that are happening now, and not worry too much about whether they may or may not get a Nature paper out of it,” says Talbot.

 

Last month, Valent’s team reported the first gene variant known to confer wheat-blast resistance (C. D. Cruz et al. Crop Sci. http://doi.org/bfk7; 2016), and field trials of crops that bear the resistance gene variant have begun in South America. But plant pathologists say that finding one variant is not enough: wheat strains must be bred with multiple genes for resistance, to stop M. oryzae quickly overcoming their defences.

 

The work could help in the Asian crisis, says Talbot. “What I would hope for out of this sorry situation,” he says, “is that there will be a bigger international effort to identify resistance genes.”


Via Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling | Genomics and metagenomics of microbes | Scoop.it
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
more...
No comment yet.
Rescooped by Bradford Condon from Plant pathogenic fungi
Scoop.it!

The invisible dimension of fungal diversity

The invisible dimension of fungal diversity | Genomics and metagenomics of microbes | Scoop.it
Taxonomy plays a central role in understanding the diversity of life, translating the products of biological exploration and discovery—specimens and observations—into systems of names that capture the relationships between species. Taxonomic names facilitate communication among scientists and the public and provide conceptual handles for complex phylogenetic hypotheses. However, taxonomy can be challenging, particularly for fungi and other microorganisms, which are morphologically simple and extremely diverse (1). Molecular environmental surveys have revealed previously unknown branches of the fungal tree of life (2–5) and illuminated biogeographic patterns across all groups of fungi (6, 7). Yet the products of this research are not being translated into formal species names, in part because of the very rules designed to facilitate taxonomy.

Via Steve Marek
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi | Genomics and metagenomics of microbes | Scoop.it
 A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.
more...
No comment yet.
Rescooped by Bradford Condon from Python Resources for Bioinformatics
Scoop.it!

A review of bioinformatic pipeline frameworks

High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I sur- vey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.

Via burkesquires
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species | Genomics and metagenomics of microbes | Scoop.it

Background: The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. 

more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Prehistoric genomes reveal the genetic foundation and cost of horse domestication | Genomics and metagenomics of microbes | Scoop.it
The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski’s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the “cost of domestication” hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome | Genomics and metagenomics of microbes | Scoop.it
Abstract: Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic se- quencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully ap- preciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Phylogenetics and the Human Microbiome

Phylogenetics and the Human Microbiome | Genomics and metagenomics of microbes | Scoop.it
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Genome Assembly of the Fungus Cochliobolus miyabeanus , and Transcriptome Analysis during Early Stages of Infection on American Wildrice ( Zizania palustris L.)

Genome Assembly of the Fungus  Cochliobolus miyabeanus , and Transcriptome Analysis during Early Stages of Infection on American Wildrice ( Zizania palustris  L.) | Genomics and metagenomics of microbes | Scoop.it
The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice ( Oryza sativa ) and two North American specialty crops, American wildrice ( Zizania palustris ) and switchgrass ( Panicum virgatum ). Despite the importance of C . miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C . miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N 50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C . miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta . A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C . miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Interconnected microbiomes and resistomes in low-income human habitats

Interconnected microbiomes and resistomes in low-income human habitats | Genomics and metagenomics of microbes | Scoop.it
Abstract:  Antibiotic-resistant infections annually claim hundreds of thousands of lives worldwide. This problem is exacerbated by exchange of resistance genes between pathogens and benign microbes from diverse habitats. Mapping resistance gene dissemination between humans and their environment is a public health priority. Here we characterized the bacterial community structure and resistance exchange networks of hundreds of interconnected human faecal and environmental samples from two low-income Latin American communities. We found that resistomes across habitats are generally structured by bacterial phylogeny along ecological gradients, but identified key resistance genes that cross habitat boundaries and determined their association with mobile genetic elements. We also assessed the effectiveness of widely used excreta management strategies in reducing faecal bacteria and resistance genes in these settings representative of low- and middle-income countries. Our results lay the foundation for quantitative risk assessment and surveillance of resistance gene dissemination across interconnected habitats in settings representing over two-thirds of the world’s population.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Scientists Say They Hope To Create A Human Genome In The Lab

Scientists Say They Hope To Create A Human Genome In The Lab | Genomics and metagenomics of microbes | Scoop.it

"Opening the door to scientific breakthroughs" vs "we don't want synthetic superbabies"

more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology | Genomics and metagenomics of microbes | Scoop.it
Click here to edit the content
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Divergent and convergent evolution of fungal pathogenicity

Divergent and convergent evolution of fungal pathogenicity | Genomics and metagenomics of microbes | Scoop.it
Abstract:
Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens, however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen-host co-speciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus-animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation.
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus | Genomics and metagenomics of microbes | Scoop.it
Abstract Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by> 3000 collections. Sources of error...
more...
No comment yet.