Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

OBJECTIVES

Sample preparation for high-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences.

METHODS

A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed using different protocols. In total, 712 sequencing libraries were investigated for viral sequence contamination.

RESULTS

Among sequences showing similarity to viruses, 493 were significantly associated with the use of laboratory components. Each of these viral sequences had sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components.

CONCLUSIONS

We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover, we show that detection can be problematic due to stochastic appearance and limited non-template controls. Although the exact origin of these viral sequences requires further research, our results support laboratory-component-linked viral sequence contamination of both biological and synthetic origin.

3D high resolution imaging for microelectronics: A multi-technique survey on copper pillars

In microelectronics, recently developed 3D integration offers the possibility to stack the dice or wafers vertically instead of putting their different parts next to one another, in order to save space. As this method becomes of greater interest, the need for 3D imaging techniques becomes higher. We here report a study about different 3D characterization techniques applied to copper pillars, which are used to stack different dice together. Destructive techniques such as FIB/SEM, FIB/FIB, and PFIB/PFIB slice and view protocols have been assessed, as well as non-destructive ones, such as laboratory-based and synchrotron-based computed tomographies. A comparison of those techniques in the specific case of copper pillars is given, taking into account the constraints linked to the microelectronics industry, mainly concerning resolution and sample throughput. Laboratory-based imaging techniques are shown to be relevant in the case of punctual analyses, while synchrotron based tomographies offer highly resolved volumes for larger batches of samples.

The genome of the simian and human malaria parasite Plasmodium knowlesi

Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.

Reverse transcription in genome evolution

As reverse transcription is predominantly performed by retrotransposable elements, the process is often entirely associated with the propagation of these elements. However, as a unique tool for transmitting information from the dynamic RNA to the more inert DNA, reverse transcription has been instrumental in shaping extant genomes. This review aims at presenting the diversity by which reverse transcription has influenced modern genomic structures.

The genome of the social amoeba Dictyostelium discoideum

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.