IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

The complete mitogenome of the Australian freshwater shrimp Paratya australiensis Kemp, 1917 (Crustacea: Decapoda: Atyidae)

The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.

The complete mitogenome of the rock pool prawn Palaemon serenus (Heller, 1862) (Crustacea: Decapoda: Palaemonidae)

The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling

BACKGROUND

Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown.

RESULTS

We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles.

CONCLUSIONS

The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.

GRASP: guided reference-based assembly of short peptides

Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release.

Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. Here we identify two linked refining mutations within ISX that interact epistatically to increase binding affinity to the dosage compensation complex. Selection has increased the frequency of this derived haplotype in the population, which is fixed at 30% of ISX insertions and polymorphic among another 41%. Sharing of this haplotype indicates that high levels of gene conversion among ISX elements allow them to ‘crowd-source’ refining mutations, and a refining mutation that occurs at any single ISX element can spread in two dimensions: horizontally across insertion sites by non-allelic gene conversion, and vertically through the population by natural selection. These results describe a novel route by which fully functional regulatory elements can arise rapidly from TEs and implicate non-allelic gene conversion as having an important role in accelerating the evolutionary fine-tuning of regulatory networks.

DOI:http://dx.doi.org/10.7554/eLife.05899.001

Mutations change genes and provide the raw material for evolution. Genes are sections of DNA that contain the instructions for making proteins or other molecules, and so determine the physical characteristics of each organism. Genetic mutations that increase an organism's number of offspring and chances of survival are more likely to be passed on to future generations. Changes to when or where a gene is switched on (so-called regulatory mutations) can also provide fitness benefits and can therefore be selected for during evolution.

Transposable elements are sequences of DNA that are also called ‘jumping genes’ because they can make copies of themselves and these copies of the transposable element can move to other locations in the genome. Some transposable elements contain sequences that switch on nearby genes. If different copies of a transposable element that contains such a regulatory sequence insert themselves in more than one place, it can result in a network of genes that can all be controlled in the same way. The regulatory sequences contained within transposable elements are not always optimal, but they can be fine-tuned through evolution.

A fruit fly called Drosophila miranda has a transposable element called ISX that has, over time, placed up to 77 regulatory sequences around one of this species' sex chromosomes. Just as in humans, female flies are XX and males are XY; but having only one copy of the X chromosome means that male flies need to increase the expression of certain genes to produce a full-dose of the molecules made by the genes. This process is called dosage compensation and in 2013 the 77 ISX regulatory sequences on the fruit fly's X chromosome were shown to help recruit the molecular machinery that carries out dosage compensation to nearby genes, albeit inefficiently. Now Ellison and Bachtrog—who also conducted the 2013 study—report how these transposable elements have been fine-tuned to make them more effective for dosage compensation.

Ellison and Bachtrog uncovered two mutations that make the ISX transposable element better at recruiting the dosage compensation molecular machinery. ISX spread around different locations along the fly's X chromosome before these mutations arose; this means that initially none of the 77 insertions carried the two mutations, but now 30% of the 77 elements have the mutations in all flies, and 41% have them in only some flies.

The same mutations have spread between the different ISX elements because transposable elements with the mutations have been used to directly convert other ISX elements without them. These mutations have also become more common in the fruit fly population by being passed on to offspring and increasing their survival. These two routes have accelerated the fine-tuning of these transposable elements for use in gene regulation. This implies that regulatory sequences derived from transposable elements evolve in a way that is fundamentally different from those that arise by other means, as the direct conversion between these insertions allows fine-tuning mutations to spread more rapidly.

DOI:http://dx.doi.org/10.7554/eLife.05899.002

Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics

The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights.

Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans.

The complete mitogenome of the Norway lobster Nephrops norvegicus (Linnaeus, 1758) (Crustacea: Decapoda: Nephropidae)

The clawed lobster Nephrops norvegicus is an important commercial species in European waters. We have sequenced the complete mitochondrial genome of the species from a partial genome scan using Next-Gen sequencing. The N. norvegicus has a mitogenome of 16,132 base pairs (71.22% A+ T content) comprising 13 protein-coding genes, 2 ribosomal subunit genes, 21 transfer RNAs, and a putative 1259 bp non-coding AT-rich region. This mitogenome is the second fully characterized for the family Nephropidae and the first for the genus Nephrops. The mitogenome gene order is identical to the Maine lobster, Homarus americanus with the exception of the possible loss of the trnI gene.

The complete mitogenome of the giant clam Tridacna squamosa (Heterodonta: Bivalvia: Tridacnidae)

The complete mitochondrial genome of the commercially and ecologically important and internationally vulnerable giant clam Tridacna squamosa was recovered by genome skimming using the MiSeq platform. The T. squamosa mitogenome has 20,930 base pairs (62.35% A+T content) and is made up of 12 protein-coding genes, 2 ribosomal subunit genes, 24 transfer RNAs, and a 2594 bp non-coding AT-rich region. The mitogenome has a relatively large insertion in the atp6 gene. This is the first mitogenome to be sequenced from the genus Tridacna, and the family Tridacnidae and represents a new gene order.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation.

Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

The intestinal protistan parasite Blastocystis is characterized by an extensive genetic variability with 17 subtypes (ST1–ST17) described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore.

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape

Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi. Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum. Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.

The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development

Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.

Disease-specific alterations in the enteric virome in inflammatory bowel disease

Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn's disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease and cohort specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.

Current strategies for mobilome research

Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.

Cetaceans evolution: insights from the genome sequences of common minke whales

Background

Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water.

Results

We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 – 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales.

Conclusions

This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1213-1) contains supplementary material, which is available to authorized users.

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement.

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising.

Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem

The Frasassi and Acquasanta Terme cave systems in Italy host isolated lithoautotrophic ecosystems characterized by sulfur-oxidizing biofilms with up to 50% S(0) by mass. The net contributions of microbial taxa in the biofilms to production and consumption of S(0) are poorly understood and have implications for understanding the formation of geological sulfur deposits as well as the ecological niches of sulfur-oxidizing autotrophs. Filamentous Epsilonproteobacteria are among the principal biofilm architects in Frasassi and Acquasanta Terme streams, colonizing high-sulfide, low-oxygen niches relative to other major biofilm-forming populations. Metagenomic sequencing of eight biofilm samples indicated the presence of diverse and abundant Epsilonproteobacteria. Populations of Sulfurovum-like organisms were the most abundant Epsilonproteobacteria regardless of differences in biofilm morphology, temperature, or water chemistry. After assembling and binning the metagenomic data, we retrieved four nearly-complete genomes of Sulfurovum-like organisms as well as a Sulfuricurvum spp. Analyses of the binned and assembled metagenomic data indicate that the Epsilonproteobacteria are autotrophic and therefore provide organic carbon to the isolated subsurface ecosystem. Multiple homologs of sulfide-quinone oxidoreductase (Sqr), together with incomplete or absent Sox pathways, suggest that cave Sulfurovum-like Epsilonproteobacteria oxidize sulfide incompletely to S(0) using either O₂ or nitrate as a terminal electron acceptor, consistent with previous evidence that they are most successful in niches with high dissolved sulfide to oxygen ratios. In contrast, we recovered homologs of the complete complement of Sox proteins affiliated Gammaproteobacteria and with less abundant Sulfuricurvum spp. and Arcobacter spp., suggesting that these populations are capable of the complete oxidation of sulfide to sulfate. These and other genomic data presented here offer new clues into the physiology and genetic potential of the largely uncultivated and ecologically successful cave Sulfurovum-like populations, and suggest that they play an integral role in subsurface S(0) formation.

Reconstructing each cell's genome within complex microbial communities-dream or reality?

As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

BACKGROUND

Estuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments.

RESULTS

De novo assembly and binning resulted in the reconstruction of 82 bacterial genomes from different redox regimes of estuary sediments. These genomes belong to 23 bacterial groups, including uncultured candidate phyla (for example, KSB1, TA06, and KD3-62) and three newly described phyla (White Oak River (WOR)-1, WOR-2, and WOR-3). The uncultured phyla are generally most abundant in the sulfate-methane transition (SMTZ) and methane-rich zones, and genomic data predict that they mediate essential biogeochemical processes of the estuarine environment, including organic carbon degradation and fermentation. Among the most abundant organisms in the sulfate-rich layer are novel Gammaproteobacteria that have genes for the oxidation of sulfur and the reduction of nitrate and nitrite. Interestingly, the terminal steps of denitrification (NO3 to N2O and then N2O to N2) are present in distinct bacterial populations.

CONCLUSIONS

This dataset extends our knowledge of the metabolic potential of several uncultured phyla. Within the sediments, there is redundancy in the genomic potential in different lineages, often distinct phyla, for essential biogeochemical processes. We were able to chart the flow of carbon and nutrients through the multiple geochemical layers of bacterial processing and reveal potential ecological interactions within the communities.

Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients

Few studies have examined the lung virome in health and disease. Outcomes of lung transplantation are known to be influenced by several recognized respiratory viruses, but global understanding of the virome of the transplanted lung is incomplete. To define the DNA virome within the respiratory tract following lung transplantation we carried out metagenomic analysis of allograft bronchoalveolar lavage (BAL), and compared with healthy and HIV+ subjects. Viral concentrates were purified from BAL and analyzed by shotgun DNA sequencing. All of the BAL samples contained reads mapping to anelloviruses, with high proportions in lung transplant samples. Anellovirus populations in transplant recipients were complex, with multiple concurrent variants. Quantitative polymerase chain reaction quantification revealed that anellovirus sequences were 56-fold more abundant in BAL from lung transplant recipients compared with healthy controls or HIV+ subjects (p < 0.0001). Anellovirus sequences were also more abundant in upper respiratory tract specimens from lung transplant recipients than controls (p = 0.006). Comparison to metagenomic data on bacterial populations showed that high anellovirus loads correlated with dysbiotic bacterial communities in allograft BAL (p = 0.008). Thus the respiratory tracts of lung transplant recipients contain high levels and complex populations of anelloviruses, warranting studies of anellovirus lung infection and transplant outcome.

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

Significance: The colonization of wounds by specific microbes or communities of microbes may delay healing and/or lead to infection-related complication. Studies of wound-associated microbial communities (microbiomes) to date have primarily relied upon culture-based methods, which are known to have extreme biases and are not reliable for the characterization of microbiomes. Biofilms are very resistant to culture and are therefore especially difficult to study with techniques that remain standard in clinical settings. Recent Advances: Culture-independent approaches employing next-generation DNA sequencing have provided researchers and clinicians a window into wound-associated microbiomes that could not be achieved before and has begun to transform our view of wound-associated biodiversity. Within the past decade, many platforms have arisen for performing this type of sequencing, with various types of applications for microbiome research being possible on each. Critical Issues: Wound care incorporating knowledge of microbiomes gained from next-generation sequencing could guide clinical management and treatments. The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing. Future Directions: As DNA sequencing technology progresses, platforms will continue to produce longer reads and more reads per run at lower costs. A major future challenge is to implement these technologies in clinical settings for more precise and rapid identification of wound bioburden.

Genome sequence of Coxiella burnetii strain Namibia

We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438 bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics.

Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment

Klbesiella pneumoniae is one of the most important human pathogens and frequently causes many diseases. To facilitate the comparative genome analysis in tigecycline resistance mechanism, we report the complete chromosomal sequence of a multidrug-resistance K. pneumoniae strain before tigecycline treatment for reference genome.

IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information

Metatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study the microbe community by sampling short reads from a mixture of mRNAs (metatranscriptomic data). As most microbial genome sequences are unknown, it would seem that de novo assembly of the mRNAs is needed. However, NGS reads are short and mRNAs share many similar regions and differ tremendously in abundance levels, making de novo assembly challenging. The existing assembler, IDBA-MT, designed specifically for the assembly of metatranscriptomic data and performs well only on high-expressed mRNAs. This article introduces IDBA-MTP, which adopts a novel approach to metatranscriptomic assembly that makes use of the fact that there is a database of millions of known protein sequences associated with mRNAs. How to effectively use the protein information is nontrivial given the size of the database and given that different mRNAs might lead to proteins with similar functions (because different amino acids might have similar characteristics). IDBA-MTP employs a similarity measure between mRNAs and protein sequences, dynamic programming techniques, and seed-and-extend heuristics to tackle the problem effectively and efficiently. Experimental results show that IDBA-MTP outperforms existing assemblers by reconstructing 14% more mRNAs.

A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum

We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis.

DOI:http://dx.doi.org/10.7554/eLife.03318.001

Microbial communities play vital roles in the environment and sustain animal and plant life. Marine microbes are part of the ocean's food chain; soil microbes support the turnover of major nutrients and facilitate plant growth; and the microbial communities residing in the human gut support digestion and the immune system, among other roles. These communities are very complex systems, often containing 1000s of different species engaged in co-dependent relationships, and are therefore very difficult to study.

The entire DNA sequence of an organism constitutes its genome, and much of this genetic information is stored in large structures called chromosomes. Examining the genome of a species can provide important clues about its lifestyle and how it evolved. To do this, DNA is extracted from cells and is then usually cut into smaller fragments, amplified, and sequenced. The small stretches of sequence obtained, called reads, are finally assembled, yielding ideally the complete genome of the organism under study.

Metagenomics attempts to interpret the combined genome of all the different species in a microbial community and has been instrumental in deciphering how the different species interact with each other. Metagenomics involves sequencing stretches of the community's DNA and matching these pieces to individual species to ultimately assemble whole genomes. While this may be a relatively straightforward task for communities that contain only a handful of members, the metagenomes derived from complex microbial communities are huge, fragmented, and incomplete. This often makes it very difficult or even nearly impossible to match the inferred DNA stretches to individual species.

A method called chromosome conformation capture (or ‘3C’ for short) can reveal the physical contacts between different regions of a chromosome and between the different chromosomes of a cell. How often each of these chromosomal contacts occurs provides a kind of physical signature to each genome and each individual chromosome within it.

Marbouty et al. took advantage of these interactions to develop a technique that combines metagenomics and chromosome conformation capture—called meta3C—that can analyze the DNA of many different species mixed together. Testing meta3C on artificial mixtures of a few species of yeast or bacteria showed that meta3C can separate the genomes of the different species without any prior knowledge of the composition of the mix. In a single experiment, meta3C can identify individual chromosomes, match each of them to its species of origin, and reveal the three-dimensional structure of each genome in the mix. Further tests showed that meta3C can also interpret more complex communities where the number and types of the species present are not known.

Meta3C holds great promise for understanding how microbial communities work and how the genomes of the species within a community are organized. However, further developments of the technique will be required to investigate communities as diverse as those present in most natural environments.

DOI:http://dx.doi.org/10.7554/eLife.03318.002

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

BACKGROUND

Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood.

RESULTS

Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes.

CONCLUSIONS

Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.

Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing

The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

Assessment of de novo assemblers for draft genomes: a case study with fungal genomes

BACKGROUND

Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evolved to assemble the reads generated by these platforms. Each tool has its own inherent advantages and disadvantages, which make the selection of an appropriate tool a challenging task.

RESULTS

We have evaluated the performance of frequently used de novo assemblers namely ABySS, IDBA-UD, Minia, SOAP, SPAdes, Sparse, and Velvet. These assemblers are assessed based on their output quality during the assembly process conducted over fungal data. We compared the performance of these assemblers by considering both computational as well as quality metrics. By analyzing these performance metrics, the assemblers are ranked and a procedure for choosing the candidate assembler is illustrated.

CONCLUSIONS

In this study, we propose an assessment method for the selection of de novo assemblers by considering their computational as well as quality metrics at the draft genome level. We divide the quality metrics into three groups: g1 measures the goodness of the assemblies, g2 measures the problems of the assemblies, and g3 measures the conservation elements in the assemblies. Our results demonstrate that the assemblers ABySS and IDBA-UD exhibit a good performance for the studied data from fungal genomes in terms of running time, memory, and quality. The results suggest that whole genome shotgun sequencing projects should make use of different assemblers by considering their merits.

Facile, high quality sequencing of bacterial genomes from small amounts of DNA

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of paired-end and single-end reads when resolving branches. Since they treat all single-end reads with overlapped length larger than a fix threshold equally, they fail to use the more confident long overlapped reads for assembling and mix up with the relative short overlapped reads. Moreover, these approaches have not been special designed for handling tandem repeats (repeats occur adjacently in the genome) and they usually break down the contigs near the tandem repeats. We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds using paired-end reads and different read overlap size ranging from O_max to O_min to resolve the gaps and branches. By constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. When the correct extension cannot be determined, PERGA will try to extend the contig by all feasible extensions and determine the correct extension by using look-ahead approach. Many difficult-resolved branches are due to tandem repeats which are close in the genome. PERGA detects such different copies of the repeats to resolve the branches to make the extension much longer and more accurate. We evaluated PERGA on both Illumina real and simulated datasets ranging from small bacterial genomes to large human chromosome, and it constructed longer and more accurate contigs and scaffolds than other state-of-the-art assemblers. PERGA can be freely downloaded at https://github.com/hitbio/PERGA.

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to metagenomic sequence reads and is frequently used in this research community. One important open problem for MetaVelvet is its low accuracy and sensitivity in detecting chimeric nodes in the assembly (de Bruijn) graph, which prevents the generation of longer contigs and scaffolds. We have tackled this problem of classifying chimeric nodes using supervised machine learning to significantly improve the performance of MetaVelvet and developed a new tool, called MetaVelvet-SL. A Support Vector Machine is used for learning the classification model based on 94 features extracted from candidate nodes. In extensive experiments, MetaVelvet-SL outperformed the original MetaVelvet and other state-of-the-art metagenomic assemblers, IDBA-UD, Ray Meta and Omega, to reconstruct accurate longer assemblies with higher N50 scores for both simulated data sets and real data sets of human gut microbial sequences.

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

Subsurface microbial life contributes significantly to biogeochemical cycling, yet it remains largely uncharacterized, especially its archaeal members. This 'microbial dark matter' has been explored by recent studies that were, however, mostly based on DNA sequence information only. Here, we use diverse techniques including ultrastuctural analyses to link genomics to biology for the SM1 Euryarchaeon lineage, an uncultivated group of subsurface archaea. Phylogenomic analyses reveal this lineage to belong to a widespread group of archaea that we propose to classify as a new euryarchaeal order ('Candidatus Altiarchaeales'). The representative, double-membraned species 'Candidatus Altiarchaeum hamiconexum' has an autotrophic metabolism that uses a not-yet-reported Factor420-free reductive acetyl-CoA pathway, confirmed by stable carbon isotopic measurements of archaeal lipids. Our results indicate that this lineage has evolved specific metabolic and structural features like nano-grappling hooks empowering this widely distributed archaeon to predominate anaerobic groundwater, where it may represent an important carbon dioxide sink.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

Within microbial communities, microorganisms adopt different lifestyle strategies to use the available resources. Here, the authors use an integrated ‘multi-omic’ approach to study niche breadth (generalist versus specialist lifestyles) in oleaginous microbial assemblages from an anoxic wastewater treatment tank.

The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)

The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.

Predicting the functional repertoire of an organism from unassembled RNA-seq data

BACKGROUND

The annotation of biomolecular functions is an essential step in the analysis of newly sequenced organisms. Usually, the functions are inferred from predicted genes on the genome using homology search techniques. A high quality genomic sequence is an important prerequisite which, however, is difficult to achieve for certain organisms, such as hybrids or organisms with a large genome. For functional analysis it is also possible to use a de novo transcriptome assembly but the computational requirements can be demanding. Up to now, it is unclear how much of the functional repertoire of an organism can be reliably predicted from unassembled RNA-seq short reads alone.

RESULTS

We have conducted a study to investigate to what degree it is possible to reconstruct the functional profile of an organism from unassembled transcriptome data. We simulated the de novo prediction of biomolecular functions for Arabidopsis thaliana using a comprehensive RNA-seq data set. We evaluated the prediction performance using several homology search methods in combination with different evidence measures. For the decision on the presence or absence of a particular function under noisy conditions we propose a statistical mixture model enabling unsupervised estimation of a detection threshold. Our results indicate that the prediction of the biomolecular functions from the KEGG database is possible with a high sensitivity up to 94 percent. In this setting, the application of the mixture model for automatic threshold calibration allowed the reduction of the falsely predicted functions down to 4 percent. Furthermore, we found that our statistical approach even outperforms the prediction from a de novo transcriptome assembly.

CONCLUSION

The analysis of an organism's transcriptome can provide a solid basis for the prediction of biomolecular functions. Using RNA-seq short reads directly, the functional profile of an organism can be reconstructed in a computationally efficient way to provide a draft annotation in cases where the classical genome-based approaches cannot be applied.

Rapid evaluation and quality control of next generation sequencing data with FaQCs

Background

Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform’s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.

Results

Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.

Conclusion

FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0366-2) contains supplementary material, which is available to authorized users.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly

Background

Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates of modern sequencers present new computational challenges in data interpretation, including mapping and de novo assembly. New lab techniques such as multiple displacement amplification (MDA) of single cells and sequence independent single primer amplification (SISPA) allow for sequencing of organisms that cannot be cultured, but generate highly variable coverage due to amplification biases.

Results

Here we introduce NeatFreq, a software tool that reduces a data set to more uniform coverage by clustering and selecting from reads binned by their median kmer frequency (RMKF) and uniqueness. Previous algorithms normalize read coverage based on RMKF, but do not include methods for the preferred selection of (1) extremely low coverage regions produced by extremely variable sequencing of random-primed products and (2) 2-sided paired-end sequences. The algorithm increases the incorporation of the most unique, lowest coverage, segments of a genome using an error-corrected data set. NeatFreq was applied to bacterial, viral plaque, and single-cell sequencing data. The algorithm showed an increase in the rate at which the most unique reads in a genome were included in the assembled consensus while also reducing the count of duplicative and erroneous contigs (strings of high confidence overlaps) in the deliverable consensus. The results obtained from conventional Overlap-Layout-Consensus (OLC) were compared to simulated multi-de Bruijn graph assembly alternatives trained for variable coverage input using sequence before and after normalization of coverage. Coverage reduction was shown to increase processing speed and reduce memory requirements when using conventional bacterial assembly algorithms.

Conclusions

The normalization of deep coverage spikes, which would otherwise inhibit consensus resolution, enables High Throughput Sequencing (HTS) assembly projects to consistently run to completion with existing assembly software. The NeatFreq software package is free, open source and available at https://github.com/bioh4x/NeatFreq.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0357-3) contains supplementary material, which is available to authorized users.

Evaluation of viral genome assembly and diversity estimation in deep metagenomes

Background

Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.

Results

We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA , which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an important factor for limiting chimericity, while scaffolding marginally improved contig length and accuracy. The genome length of the various viruses in the metagenomes did not significantly affect genome reconstruction, but the co-existence of highly similar genomes was detrimental. When evaluating diversity estimation tools, we found that PHACCS results were more accurate than those from CatchAll and clustering, which were both orders of magnitude above expected.

Conclusions

Assemblers designed specifically for the analysis of metagenomes should be used to facilitate the creation of high-quality long contigs. Despite the high coverage possible, scientists should not expect to always obtain complete genomes, because their reconstruction may be hindered by co-existing species bearing highly similar genomic regions. Further development of metagenomics-oriented assemblers may help bypass these limitations in future studies. Meanwhile, the lack of fully reconstructed communities keeps methods to estimate viral diversity relevant. While none of the three methods tested had absolute precision, only PHACCS was deemed suitable for comparative studies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-989) contains supplementary material, which is available to authorized users.