BioMed Central Blog
False duplications in genome assemblies
David Kelley and Steven Salzberg at the University of Maryland have developed a pipeline to correct misassembles due to false duplications, in a study published today in Genome Biology. Diploid genomes harbour a significant amount of variation between homologous chromosomes. This causes problems for genome assembly algorithms which may construct two DNA sequences corresponding to one divergent region and incorporate both into an assembly as a false segmental duplication.
Their approach is to align DNA sequence fragments to the surrounding sequence, using mate pair information, to determine whether duplicated segments should be merged into one copy. Mate pairs are two sequence reads derived from the same region of DNA and this study is the first time in which mate pair reads have been used to detect duplications. Kelley and Salzberg apply their pipeline to the cow, chimpanzee, dog and chicken genomes and they identify many single copy regions that have been falsely incorporated as segmental duplications in these genome assemblies, which also allows previously undetected polymorphisms to be identified. This promises to be a valuable method for correcting existing errors in many genome assemblies and to control for misassembly errors in future genome sequencing efforts.
Posted by Emma Ralph at 11:50 Comments (0)
Genome Biology recently published an article from Alicia Oshlack and colleagues in which they describe an approach for performing Gene Ontology analysis on RNA-seq data. RNA-seq is an emerging technology for monitoring gene expression levels by directly sequencing the mRNA molecules in a sample, and is likely to overtake microarrays as the technique of choice for gene expression profiling. Now, Genome Biology has published another innovative method, this time for normalizing RNA-seq data. This method is much needed and will be embraced by the genomics community as, until now, methods for normalizing RNA-seq data have often relied on tools that were based on those developed for microarray data.
A common approach for normalizing RNA-seq data has been to consider the expression of an individual gene relative to the global gene expression levels. In her latest paper, Oshlack, at the Walter and Eliza Hall Institute in Melbourne, Australia, shows that this is not always appropriate. In particular, if one tissue has a small number of genes that are significantly differentially expressed compared with another tissue then these can affect whether or not other genes in the sample are determined as being differentially expressed, often leading to implausible results. The paper demonstrates again the need for new statistical techniques to fully exploit the powerful RNA-seq technology, as well as providing a useful tool for doing this.
Posted by Andrew Cosgrove at 17:32 Comments (0)
Pea aphid immune system genomics
Today an annotation of the pea aphid immune system has been published in Genome Biology by Nicole Gerardo and colleagues. This coincides with the publication of the draft pea aphid genome sequence from the International Aphid Genomics Consortium in PLoS Biology.
Due to its unusual process of metamorphosis the pea aphid provides interesting insights into insect development and, as a major vector of plant viruses and cause of crop damage, further understanding of pea aphid biology may lead to the development of control strategies. Pea aphids also display other fascinating biological properties, such as phenotypic plasticity, a lifecycle that alternates between parthenogenic and sexual reproduction, and they have co-evolved with symbiotic bacteria.
In their Genome Biology paper, which is also discussed in a Research Highlight in Genome Biology, Gerardo and colleagues perform an extensive manual annotation of the immune and stress response genes present in the pea aphid genome and they also analyse gene and protein expression in pathogen infected aphids to gain insights into how they respond to challenges to their immune system. They find that pea aphids lack many immune response genes found in other insect species and that their response to pathogen attack is more limited than in other insect species. These features may mirror those seen in other insects or they may be due to the unique biology of pea aphid and their relationship with symbiotic bacteria. Whatever the case turns out to be, the general view of insect immunity may not be as widely applicable as previously thought.
Posted by Emma Ralph at 18:02 Comments (0)
GOseq – a new method for Gene Ontology analysis of RNA-seq data
Until recently, microarrays have been the method of choice for transcriptional profiling. The advent of next generation sequencing technologies however has seen the rise of direct sequencing of mRNA (RNA-seq) as a new method for such profiling. In a recent publication in Genome Biology, Alicia Oshlack and colleagues at the Walter and Eliza Hall Institute in Melbourne, Australia have developed a new method for performing Gene Ontology analysis of RNA-seq data, called GOseq.
GOseq identifies whether a given transcriptional profile is over-represented with transcripts associated with specific biological processes. Up until now, statistical methods, such as this, used for analysing RNA-seq data have generally been modifications of methods developed for use with microarray data. Oshlack, however, shows that statistical methods are not interchangeable between the two techniques; in particular, there is a bias inherent in RNA-seq data whereby highly-expressed transcripts are more likely to be called as being differentially expressed compared with short or less highly-expressed genes. The GOseq algorithm takes this into account, thus correcting the bias and providing a more reliable readout. As well as providing a useful new tool, this paper highlights the need for new statistical analysis techniques tailored specifically for the new technology of RNA-seq.
Given the extent to which RNA-seq is being embraced by the genomics community, for example in defining alternative transcripts, this method is a welcome addition to a growing field.
Posted by Andrew Cosgrove at 16:44 Comments (0)
Silence launches with BioMed Central
Silence, a new open access journal covering all aspects of genetic and epigenetic control mediated by RNA, has launched with Phil Zamore and David Baulcombe as Editors-in-Chief. Silence is supported by an outstanding international Editorial Board.
The first articles published in Silence today cover a range of RNA regulatory areas. Mueller et al describe the Solution structure of the Drosha double-stranded RNA-binding domain, while Dr Parker reviews the role of argonaute as a key component in RNA slicing, particularly in light of recent work by Patel et al.
Silence aims to become the journal for the RNA silencing and non-coding RNA community, bringing together researchers working on all model organisms, and from both academia and industry.
If you are interested in RNA silencing, please visit the journal homepage to read our latest articles and submit work of your own. If you would like to receive regular emails detailing the most recently published articles please register for email alerts. We will also be highlighting interesting findings and news on the journal blog site; please sign up for RSS feeds to stay abreast of the latest news in this field.
Posted by Emma Pettengale at 14:24 Comments (0)
Can plausibility be quantified?
As the probability of a specific occurrence or outcome tends towards 0 it becomes less likely, but even the most unlikely events rarely attain classification as an absolute impossibility. However, there appears to be a need to address the misunderstanding that theoretical possibility is the same as plausibility, if only to save the funds spent, and the subsequent time of peer reviewers, on research that pushes the boundaries of credibility.
A solution to this problem has recently been proposed in an article published in Theoretical Biology & Medical Modelling. Dr Abel draws upon previous descriptions and concepts in his article The Universal Plausibility Metric (UPM) & Principle (UPP) and describes an equation, featuring the pre-defined concepts of UPM and UPP, to determine the threshold for implausibility and suggests that it should be used to assess the plausibility of a hypothesis as part of the methods for future research.
Although the biggest impact of this application would be within the fields of astrobiology and life-origin research, it could be applied in all fields of scientific investigation.
Should this equation be used to identify whether a hypothesis is too far-fetched to justify scientific expenditure and investigation? Or do we have a need to test the nigh on impossible in order to satisfy curiosity and to continue to delve into the unknown and improbable?
Posted by Lisa Phelps at 11:11 Comments (0)
Designer probiotics: the future or too much to stomach?
Although the benefits of probiotics have been postulated for more than 100 years, there has been an increasing interest in the effects of probiotics on ill health and general well being over recent years.
Studies have shown positive outcomes of probiotics in the treatment and prevention of gastrointestinal infections and disease. But are generic probiotics enough? In the review “Probiotics and gastrointestinal disease: successes, problems and future prospects” published in Gut Pathogens, Eamonn Culligan et al. review the treatment of various GI disorders with specific probiotic strains. They also discuss whether the future lies with designer probiotics, which are engineered to specifically target a particular toxin or pathogen, but raise concerns of a negative public reaction to the development of this possible course of treatment.
Will designer probiotics be the future treatment of GI disorders? Or will public resistance for genetically modified organisms hinder its progress?
Posted by Lisa Phelps at 17:33 Comments (0)
Biological adventures into the world of cloud computing
Cloud computing is becoming an increasingly popular phenomenon in the world of computing. Analysing data in ‘the cloud’ involves using a self-service internet infrastructure, where you pay-as-you-go and use only what you need, all managed by the third party provider, typically Amazon or Google.
This technology has so far not been utilised for biological computing applications. The potential uses of cloud computing to analyse the mass of data pouring out of next-generation sequencing projects has, however, been a topic of hot debate in recent months amongst biologists and computational biologist alike.
In this month’s issue of Genome Biology, Ben Langmead and colleagues, from the University of Maryland and the John Hopkins Bloomberg School of Public Health, present the Crossbow algorithm for the alignment of whole-genome sequence data and the mapping of genetic variation information, such Single Nucleotide Polymorphisms (SNPs). Crossbow combines the alignment speed of the Bowtie algorithm, together with the SNP calling accuracy of the SOAPsnp algorithm, and allows them to be run on any publicly-available cloud computing cluster.
In the article presenting Crossbow Langmead and colleagues demonstrate how data from a 38-fold coverage of the human genome can be aligned, and the SNPs mapped, in less than 3 hours and for only US$ 85 using the Amazon cloud.
The authors believe this first demonstration of software for biological applications being able to utilise the technology of cloud computing will revolutionise the way we analyse our biological data.
Crossbow is open source and freely available to download here, as well as being provided online with the Genome Biology article.
Liz Gaskell, Senior Assistant Editor, Genome Biology.
Posted by Elisabeth Gaskell at 16:17 Comments (0)
The Coral genetic linkage map – an essential resource for Coral biology
Coral reefs are diverse marine ecosystems. Overfishing, pollution and the effects of climate change including, ocean acidification (as a result of rising carbon dioxide levels) are destroying these precious environments. Reefs are being lost at an alarming rate and understanding whether/how coral can adapt to these changes could provide clues for aiding their preservation.
In this month’s issue of Genome Biology, Mikhail Matz and colleagues from the University of Texas present a high-resolution genetic linkage map of the reef-building coral Acropora millepora, the first for any coral or any non-bilaterian animal, and the most basal metazoan genetic linkage map to date. This linkage map will enable the identification of the quantitative trait loci (QTLs) associated with adaptation-relevant physiological traits, as well as facilitating population genomics studies and coral genome assembly.
As well as facilitating future studies into coral genomics, biology and ecology, the linkage map itself reveals insights into coral biology. The consensus genetic linkage map contains more than 400 markers distributed over 14 linkage groups. Matz and colleagues also produced separate male and female linkage maps, and found that the female map was 1.3x longer than that of the male, suggesting that this coral may possess sex-specific differences in recombination. The coral map also revealed syntenic regions with other metazoan genomes, allowing the authors to build a picture of the architecture of the ancestral metazoan genome.
This new genetic linkage map provides an important resource for future studies on coral genome structure and enhances our understanding of metazoan genome evolution
You can read the article by Matz and colleagues in this month’s issue of Genome Biology.
Clare Hinkley, Senior Editor, Genome Biology
Posted by Elisabeth Gaskell at 18:01 Comments (0)
Announcing the launch of Allergy, Asthma & Clinical Immunology
Allergy, Asthma & Clinical
Immunology, the official journal of the Canadian Society of Allergy and
Clinical Immunology (CSACI), has now
commenced publication with BioMed Central, having transferred to our open access
publishing format with the aim of increasing the success of the
journal.Posted by Sally Robertson at 14:02 Comments (0)
A new method for next-generation re-sequencing of mouse chromosomes
A team led by David Adams from The Wellcome Trust Sanger Institute and colleagues at the MRC Mammalian Genetics Unit and Case Western Reserve University demonstrate the application of next-generation sequencing to re-sequence whole mouse chromosomes for genetic studies in an article published today in Genome Biology.
Currently only a single mouse genome sequence is available – that of the mouse strain C57BL/6J. This sequence is rather different from the sequence of other mouse strains that are commonly used in genetic studies. In the Genome Biology article, assemblies of chromosome 17 from the A/J and CAST/Ei strains were constructed from high-throughput sequence data at a depth of at least 22X. AJ is a classical laboratory strain, which is closely related to the ‘reference’ C57BL/6J strain, while the CAST/Ei strain is highly divergent from the reference as it was derived from a wild isolate. The authors identified single nucleotide polymorphisms (SNPs) and structural variants in the chromosome 17 assemblies and also demonstrate how these sequences can be used to profile quantitative trait loci genes. New algorithms for identifying copy number variations (CNVs) and for SNP filtering, as well as an assembly algorithm are also presented.
The new approaches demonstrated here open the way for a new era of rodent functional genomics.
Read the article by Adams and colleagues in Genome Biology.
Posted by Emma Ralph at 15:49 Comments (0)
EvoDevo is now accepting submissions!
EvoDevo, a new open access journal on the hot topic
of evolutionary developmental biology, is ready to
accept submissions.
Topics of interest include comparative gene function and expression, homology and character evolution, comparative genomics, phylogenetics and palaeontology.
This soon-to-be launched BioMed Central journal is overseen by co-Editors-in-Chief Mark Q Martindale (University of Hawaii, USA) and Max Telford (University College London, UK), who are supported by an expert Editorial Board.
For more information on EvoDevo please visit the journal website or contact the Editorial Office. Why not register for updates keeping you abreast of any journal developments?
Submit your research to EvoDevo and take advantage of an efficient online submission process, a rapid, high quality peer-review service and high visibility. There are no extra charges or limits on the number of color figures or movies you wish to include.
Posted by Emma Pettengale at 12:41 Comments (0)
Mapping differences in 1001 genomes – multiple genomes are better than one
Sequencing multiple individuals from a single species allows researchers to ask key biological questions regarding, for example, the diversity and population genetics of that species. The answers to many of these questions rely on the accurate mapping of polymorphisms between individual genomes.
The Human 1000 genomes and the Arabidopsis 1001 genomes projects are taking advantage of the rapid and increasingly affordable next-generation sequencing technologies to do just that. Millions of reads of sequence data can be generated in a relatively short period of time and once this information is pieced together, comparisons of multiple genomes from individuals of a single species are possible.
The advent of these ambitious sequencing projects requires concurrent advances in the software needed to analyse these data. Existing software for aligning short-read sequence data from next generation sequencing technologies have previously relied on aligning new sequences to a single reference genome.
In Genome Biology this month, Detlef Weigel, the Director of the Department of Molecular Biology at the Max Planck Institute for Developmental Biology in Tübingen, and colleagues introduce GenomeMapper, a new, open-source software for the assembly of short-read sequence data to multiple reference genomes at one time; they demonstrate the power of this tool by applying it to new sequence data from the Arabidopsis 1001 genomes project. GenomeMapper greatly increases our ability to compare genomes and the detection of polymorphisms between large numbers of individuals is now possible on a scale that was unimaginable previously.
You can read the full article from Detlef Weigel and colleagues on the Genome Biology website and the GenomeMapper software can be freely downloaded here.
You can also find out more about the Arabidopsis 1001 genomes project from their website http://1001genomes.org/index.html and read an opinion article highlighting the plans for this project, published in the May 2009 issue of Genome Biology.
Posted by Elisabeth Gaskell at 18:10 Comments (0)
A special series of companion papers from the FANTOM4 consortium
Genome Biology and BMC
Bioinformatics have published the first articles in a new
cross-journal article series reporting results from FANTOM4,
the latest research project from the FANTOM consortium.
FANTOM (Functional Annotation of Mouse) is an international collaborative research project initiated and organized by the RIKEN Omics Science Center in Yokohama, Japan. Previous work from the FANTOM consortium has focused on identifying the transcribed components of mammalian cells. FANTOM4 builds on this work, using novel methods to define how these cellular components are regulated and work together as a biological network in the acute myeloid leukemia cell line THP-1.
Among
the first FANTOM4 papers to be published in Genome
Biology is a description of a suite of computer
programs from Josee Dostie and colleagues which allow chromatin conformation
signatures to be identified. In the same journal, Alistair Forrest
and colleagues describe EdgeExpressDB,
a new database and associated tools for interpreting biological networks
and comparing large high-throughput expression datasets. Further
work published in BMC
Bioinformatics by John Quackenbush and colleagues outlines two
new data-driven normalization strategies for high-throughput
real-time quantitative
PCR data. Additional research articles in this
article series will be published over coming months.
The FANTOM4 papers, including three additional companion articles just published
in Nature Genetics, are put in context
by Phil Kapranov’s minireview,
which is also published in the latest issue of Genome Biology.
Posted by Ruth Rowland at 21:34 Comments (0)
Can satellites measure carbon emissions from deforestation?
A recent article published in Carbon
Balance & Management suggests the use of satellite technology for
monitoring global carbon stocks.
Deforestation and forest degradation accounts for nearly a third of anthropogenic carbon emissions and reduction of these emissions is an important aspect of climate change policy. However, effective management and reduction of these emissions relies on an accurate method for mapping and monitoring the carbon stocks of the forested regions of the world.
Carbon stocks are traditionally mapped using field measurements of vegetation or land cover types to measure the above ground biomass of an area, as satellite data was thought to be inadequate for the task. A recent review published in Carbon Balance and Management and featured on Mongabay challenges this consensus.
Mapping and monitoring carbon
stocks with satellite observations: a comparison of methods
Scott J Goetz, Alessandro Baccini, Nadine T Laporte, Tracy
Johns, Wayne Walker, Josef Kellndorfer, Richard A Houghton, Mindy Sun
Carbon Balance and Management 2009, 4:2
(25 March 2009)
In their article, Dr Goetz et al compare traditional mapping methods with new methods that directly utilize satellite measurements from several different satellite sources. They conclude that a combination of remote sensing methods provide more coherent maps of carbon stocks and also removes the uncertainty and ambiguity associated with purely traditional approaches.
This improved method for monitoring carbon stock comes at a crucial time for addressing global climate change with several meetings on the topic being held throughout the year leading up to the United Nations Framework Convention on Climate Change in Copenhagen in December. You can stay up to date with the latest articles from Carbon Balance & Management by signing up for email article alerts.
Posted by Anne Braae at 09:54 Comments (0)