The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Principle Component Analysis

Scientific journals and regulatory agencies want reliable clinical trials, but the definition of 'reliable' isn't necessarily the same for both parties.

/pdf/in-the-eye-of-the-beholder-223zdu5c31.pdf

In the Eye of the Beholder

Pollution of lakes and rivers. A paleoenvironmental perspective

Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome sequencing is growing steadily. Ancient DNA fragments are typically ultrashort molecules and carry extensive amounts of chemical damage accumulated after death. Their extraction, manipulation and authentication require specific experimental wet-laboratory and dry-laboratory procedures before patterns of genetic variation from past individuals, populations and species can be interpreted. Ancient DNA data help to address an entire array of questions in anthropology, evolutionary biology and the environmental and archaeological sciences. The data have revealed a considerably more dynamic past than previously appreciated and have revolutionized our understanding of many major prehistoric and historic events. This Primer provides an overview of concepts and state-of-the-art methods underlying ancient DNA analysis and illustrates the diversity of resulting applications. The article also addresses some of the ethical challenges associated with the destructive analysis of irreplaceable material, emphasizes the need to fully involve archaeologists and stakeholders as part of the research design and analytical process, and discusses future perspectives. This Primer outlines the best ways to find, handle and analyse ancient DNA from various sources. The authors summarize ethical considerations and the importance of working closely with all stakeholders, including archaeologists, curators and descendant communities.

Ancient DNA analysis

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.

/pdf/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-3natzwabxr.pdf

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

The shells of marine mollusks represent promising metagenomic archives of the past, adding to bones, teeth, hairs, and environmental samples most commonly examined in ancient DNA research. Seminal work has established that DNA recovery from marine mollusks depends on their shell microstructure, preservation and disease state, and that authentic ancient DNA could be retrieved from specimens as old as 7,000 years. Here, we significantly push the temporal limit for shell DNA recovery to 100,000 years with the successful genetic characterization of one Portlandia arctica and one Mytilus mussel sample collected within a dated permafrost layer from the Taimyr Peninsula, Russia. We expand the analysis of ancient DNA in carbonate shells to a larger number of genera (Arctica, Cernuella, Crassostrea, Dreissena, Haliotis, Lymnaea, Margaritifera, Pecten, Ruditapes, Venerupis) from marine, freshwater and terrestrial environments. We demonstrate that DNA from ancient shells can provide sufficient resolution for taxonomic, phylogenetic and/or population assignment. Our results confirm mollusk shells as long-term DNA reservoirs, opening new avenues for the investigation of environmental changes, commercial species management, biological invasion, and extinction. This is especially timely in light of modern threats to biodiversity and ecosystems.

/pdf/unveiling-the-ecological-applications-of-ancient-dna-from-2yv1nkiduo.pdf

Unveiling the Ecological Applications of Ancient DNA from Mollusk Shells

The appearance of rich and diverse funerary practices is one of the hallmarks of the Late Epipalaeolithic Natufian in the Levant. Numerous burials at a number of sites excavated mostly in the Medit...

/pdf/ochre-ground-stone-and-wrapping-the-dead-in-the-late-uxdvcknl4t.pdf

Ochre, Ground Stone, and Wrapping the Dead in the Late Epipalaeolithic (Natufian) Levant: Revealing the Funerary Practices at Shubayqa 1, Jordan

Principal component analysis (PCA) was performed on chemical data of two sediment cores from an urban freshwater lake in Copenhagen, Denmark. X-ray fluorescence (XRF) core scanning provided the underlying datasets on 13 variables (Si, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb, Cd, and Pb). Principal component analysis helped to trace geochemical patterns and temporal trends in lake sedimentation. The PCA models explained more than 80 % of the original variation in the datasets using only two or three principal components. The first principal component (PC1) was mostly associated with geogenic elements (Si, K, Fe, Rb) and characterized the content of minerogenic material in the sediment. In the case of both cores, PC2 was a good descriptor emphasized as the contamination component. It showed strong linkages with heavy metals (Cu, Zn, Pb), disclosing changing heavy-metal contamination trends across different depths. The sediments featured a temporal association with contaminant dominance. Lead contamination was superseded by zinc within the compound pattern which was linked to changing contamination sources over time. Principal component analysis was useful to visualize and interpret geochemical XRF data while being a straightforward method to extract contamination patterns in the data associated with temporal elemental trends in lake sediments.

https://link.springer.com/content/pdf/10.1007%2Fs11270-014-2221-5.pdf

Peter Ilsøe

Papers

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

Unveiling the Ecological Applications of Ancient DNA from Mollusk Shells

Ochre, Ground Stone, and Wrapping the Dead in the Late Epipalaeolithic (Natufian) Levant: Revealing the Funerary Practices at Shubayqa 1, Jordan

Pattern Recognition on X-ray Fluorescence Records from Copenhagen Lake Sediments Using Principal Component Analysis