Stephan C Schuster

Publications of Stephan C Schuster

• Chloride and organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus.

  Authors: Stephan H Saum, Friedhelm Pfeiffer, Peter Palm, Markus Rampp, Stephan C Schuster, Volker Müller, Dieter Oesterhelt

  Environmental microbiology. 05/2012;

  Salt acclimation in moderately halophilic bacteria is the result of action of a grand interplay orchestrated by signals perceived from the environment. To elucidate the cellular players involved inSalt acclimation in moderately halophilic bacteria is the result of action of a grand interplay orchestrated by signals perceived from the environment. To elucidate the cellular players involved in sensing and responding to changing salinities we have determined the genome sequence of Halobacillus halophilus, a Gram-positive moderate halophilic bacterium that has a strict requirement for the anion chloride. Halobacillus halophilus synthesizes a multitude of different compatible solutes and switches its osmolyte strategy with the external salinity and growth phase. Based on the emerging genome sequence, the compatible solutes glutamate, glutamine, proline and ectoine have already been experimentally studied. The biosynthetic routes for acetyl ornithine and acetyl lysine are also delineated from the genome sequence. Halobacillus halophilus is nutritionally very versatile and most compatible solutes cannot only be produced but also used as carbon and energy sources. The genome sequence unravelled isogenes for many pathways indicating a fine regulation of metabolism. Halobacillus halophilus is unique in integrating the concept of compatible solutes with the second fundamental principle to cope with salt stress, the accumulation of molar concentrations of salt (Cl(-) ) in the cytoplasm. Extremely halophilic bacteria/archaea, which exclusively rely on the salt-in strategy, have a high percentage of acidic proteins compared with non-halophiles with a low percentage. Halobacillus halophilus has an intermediate position which is consistent with its ability to integrate both principles.

• Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.

  Authors: Gue Su Chang, Angelika A Noegel, Travis N Mavrich, Rolf Muller, Lynn P Tomsho, Elissa Ward, Marius Felder, Cizhong Jiang, Ludwig Eichinger, Gernot Glockner, Stephan C Schuster, B Franklin Pugh

  Genome research. 03/2012;

  Dictyostelium discoideum is a member of the amoebozoa that exists in both a free-living unicellular and a multi-cellular form. It is situated in a deep branch in the evolutionary tree, and isDictyostelium discoideum is a member of the amoebozoa that exists in both a free-living unicellular and a multi-cellular form. It is situated in a deep branch in the evolutionary tree, and is particularly noteworthy in having a very A/T-rich genome. Dictyostelium provides an ideal system to examine the extreme to which nucleotide bias may be employed in organizing promoters, genes, and nucleosomes across a genome. We find that Dictyostelium genes are demarcated precisely at their 5' ends by poly-T tracts and precisely at their 3' ends by poly-A tracts. These tracts are also associated with nucleosome-free regions, and are embedded with precisely positioned TATA boxes. Homo- and heteropolymeric tracts of A and T demarcate nucleosome border regions. Together these findings reveal the presence of a variety of functionally distinct polymeric A/T elements. Strikingly, Dictyostelium chromatin may be organized in di-nucleosome units, but is otherwise organized as in animals. This includes a +1 nucleosome in a position, that predicts the presence of a paused RNA polymerase. Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and nucleosome positioning may have co-evolved with animal multi-cellularity.

• Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genome.

  Authors: Daniel Elleder, Oekyung Kim, Abinash Padhi, Jason G Bankert, Ivan Simeonov, Stephan C Schuster, Nicola E Wittekindt, Susanne Motameny, Mary Poss

  Journal of virology. 12/2011; 86(5):2787-96.

  Endogenous retroviruses constitute a significant genomic fraction in all mammalian species. Typically they are evolutionarily old and fixed in the host species population. Here we report on a novelEndogenous retroviruses constitute a significant genomic fraction in all mammalian species. Typically they are evolutionarily old and fixed in the host species population. Here we report on a novel endogenous gammaretrovirus (CrERVγ; for cervid endogenous gammaretrovirus) in the mule deer (Odocoileus hemionus) that is insertionally polymorphic among individuals from the same geographical location, suggesting that it has a more recent evolutionary origin. Using PCR-based methods, we identified seven CrERVγ proviruses and demonstrated that they show various levels of insertional polymorphism in mule deer individuals. One CrERVγ provirus was detected in all mule deer sampled but was absent from white-tailed deer, indicating that this virus originally integrated after the split of the two species, which occurred approximately one million years ago. There are, on average, 100 CrERVγ copies in the mule deer genome based on quantitative PCR analysis. A CrERVγ provirus was sequenced and contained intact open reading frames (ORFs) for three virus genes. Transcripts were identified covering the entire provirus. CrERVγ forms a distinct branch of the gammaretrovirus phylogeny, with the closest relatives of CrERVγ being endogenous gammaretroviruses from sheep and pig. We demonstrated that white-tailed deer (Odocoileus virginianus) and elk (Cervus canadensis) DNA contain proviruses that are closely related to mule deer CrERVγ in a conserved region of pol; more distantly related sequences can be identified in the genome of another member of the Cervidae, the muntjac (Muntiacus muntjak). The discovery of a novel transcriptionally active and insertionally polymorphic retrovirus in mammals could provide a useful model system to study the dynamic interaction between the host genome and an invading retrovirus.

• Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria.

  Authors: Amaya M Garcia Costas, Zhenfeng Liu, Lynn P Tomsho, Stephan C Schuster, David M Ward, Donald A Bryant

  Environmental microbiology. 09/2011; 14(1):177-90.

  Candidatus Chloracidobacterium thermophilum, which naturally inhabits microbial mats of alkaline siliceous hot springs in Yellowstone National Park, is the only known chlorophototroph in the phylumCandidatus Chloracidobacterium thermophilum, which naturally inhabits microbial mats of alkaline siliceous hot springs in Yellowstone National Park, is the only known chlorophototroph in the phylum Acidobacteria. The Ca. C. thermophilum genome was composed of two chromosomes (2,683,362 bp and 1,012,010 bp), and both encoded essential genes. The genome included genes to produce chlorosomes, the Fenna-Matthews-Olson protein, bacteriochlorophylls a and c as principal pigments, and type-1, homodimeric reaction centres. Ca. C. thermophilum is an aerobic photoheterotroph that lacks the ability to synthesize several essential nutrients. Key genes of all known carbon fixation pathways were absent, as were genes for assimilatory nitrate and sulfate reduction and vitamin B(12) synthesis. Genes for the synthesis of branched-chain amino acids (valine, isoleucine and leucine) were also absent, but genes for catabolism of these compounds were present. This observation suggested that Ca. C. thermophilum may synthesize branched-chain amino acids from an intermediate(s) of the catabolic pathway by reversing these reactions. The genome encoded an aerobic respiratory electron transport chain that included NADH dehydrogenase, alternative complex III and cytochrome oxidase. The chromosomes of the laboratory isolate were compared with assembled, metagenomic scaffolds from the major Ca. C. thermophilum population in hot-spring mats. The larger chromosomes of the two populations were highly syntenous but significantly divergent (~13%) in sequence. In contrast, the smaller chromosomes have undergone numerous rearrangements, contained many transposases, and might be less constrained by purifying selection than the large chromosomes. Some transposases were homologous to those of mat community members from other phyla.

• A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T.

  Authors: Karin Schwibbert, Alberto Marin-Sanguino, Irina Bagyan, Gabriele Heidrich, Georg Lentzen, Harald Seitz, Markus Rampp, Stephan C Schuster, Hans-Peter Klenk, Friedhelm Pfeiffer, Dieter Oesterhelt, Hans Jörg Kunte

  Environmental microbiology. 08/2011; 13(8):1973-94.

  The halophilic γ-proteobacterium Halomonas elongata DSM 2581(T) thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated accordingThe halophilic γ-proteobacterium Halomonas elongata DSM 2581(T) thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to halophilic environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin and health care applications and is thus produced annually on a scale of tons in an industrial process using H. elongata as producer strain. This paper presents the complete genome sequence of H. elongata (4,061,296 bp) and includes experiments and analysis identifying and characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine degradation and its cyclic connection to ectoine synthesis. The degradation of ectoine (doe) proceeds via hydrolysis of ectoine (DoeA) to Nα-acetyl-L-2,4-diaminobutyric acid, followed by deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was derived that can be used to understand the way H. elongata survives under varying salt stresses and that provides a basis for a model-driven improvement of industrial ectoine production.

• Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

  Authors: Weisheng Wu, Yong Cheng, Cheryl A Keller, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, Christine M Dorman, Kuan-Bei Chen, Daniela Drautz [......] Terrence S Furey, Manolis Kellis, Webb Miller, James Taylor, Stephan C Schuster, Yu Zhang, Francesca Chiaromonte, Gerd A Blobel, Mitchell J Weiss, Ross C Hardison

  Genome research. 07/2011; 21(10):1659-71.

  Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordinationInterplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.

• Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).

  Authors: Webb Miller, Vanessa M Hayes, Aakrosh Ratan, Desiree C Petersen, Nicola E Wittekindt, Jason Miller, Brian Walenz, James Knight, Ji Qi, Fangqing Zhao [......] Stephen Pyecroft, Kristofer M Helgen, Arthur M Lesk, Thomas H Pringle, Nick Patterson, Yu Zhang, Alexandre Kreiss, Gregory M Woods, Menna E Jones, Stephan C Schuster

  Proceedings of the National Academy of Sciences of the United States of America. 06/2011; 108(30):12348-53.

  The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to rejectThe Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations.

• Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat.

  Authors: Zhenfeng Liu, Christian G Klatt, Jason M Wood, Douglas B Rusch, Marcus Ludwig, Nicola Wittekindt, Lynn P Tomsho, Stephan C Schuster, David M Ward, Donald A Bryant

  The ISME journal. 06/2011; 5(8):1279-90.

  The phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted from matThe phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted from mat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in one diel cycle, and these RNA samples were analyzed by both pyrosequencing and SOLiD technologies. Pyrosequencing was used to assess the community composition, which showed that ~84% of the rRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi and Acidobacteria. Transcription of photosynthesis-related genes conclusively demonstrated the phototrophic nature of two newly discovered populations; these organisms, which were discovered through metagenomics, are currently uncultured and previously undescribed members of Chloroflexi and Chlorobi. Data sets produced by SOLiD sequencing of complementary DNA provided >100-fold greater sequence coverage. The much greater sequencing depth allowed transcripts to be detected from ~15,000 genes and could be used to demonstrate statistically significant differential transcription of thousands of genes. Temporal differences for in situ transcription patterns of photosynthesis-related genes suggested that the six types of chlorophototrophs in the mats may use different strategies for maximizing their solar-energy capture, usage and growth. On the basis of both temporal pattern and transcript abundance, intra-guild gene expression differences were also detected for two populations of the oxygenic photosynthesis guild. This study showed that, when community-relevant genomes and metagenomes are available, SOLiD sequencing technology can be used for metatranscriptomic analyses, and the results suggested that this method can potentially reveal new insights into the ecophysiology of this model microbial community.

• Integrative analysis of environmental sequences using MEGAN4.

  Authors: Daniel H Huson, Suparna Mitra, Hans-Joachim Ruscheweyh, Nico Weber, Stephan C Schuster

  Genome research. 06/2011; 21(9):1552-60.

  A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic andA major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

• Ancestral polyploidy in seed plants and angiosperms.

  Authors: Yuannian Jiao, Norman J Wickett, Saravanaraj Ayyampalayam, André S Chanderbali, Lena Landherr, Paula E Ralph, Lynn P Tomsho, Yi Hu, Haiying Liang, Pamela S Soltis, Douglas E Soltis, Sandra W Clifton, Scott E Schlarbaum, Stephan C Schuster, Hong Ma, Jim Leebens-Mack, Claude W dePamphilis

  Nature. 05/2011; 473(7345):97-100.

  Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especiallyWhole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

• Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

  Authors: Philipp Engel, Walter Salzburger, Marius Liesch, Chao-Chin Chang, Soichi Maruyama, Christa Lanz, Alexandra Calteau, Aurélie Lajus, Claudine Médigue, Stephan C Schuster, Christoph Dehio

  PLoS genetics. 01/2011; 7(2):e1001296.

  Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process isAdaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.

• The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.

  Authors: Bettina Siebers, Melanie Zaparty, Guenter Raddatz, Britta Tjaden, Sonja-Verena Albers, Steve D Bell, Fabian Blombach, Arnulf Kletzin, Nikos Kyrpides, Christa Lanz, André Plagens, Markus Rampp, Andrea Rosinus, Mathias von Jan, Kira S Makarova, Hans-Peter Klenk, Stephan C Schuster, Reinhard Hensel

  PloS one. 01/2011; 6(10):e24222.

  Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. ItsHere, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is strictly anaerobic and sulfur-dependent with optimal growth at 86°C and pH 5.6. One particular feature is the great metabolic versatility, which is not accompanied by a distinct increase of genome size or information density as compared to other Crenarchaeota. T. tenax is able to grow chemolithoautotrophically (CO₂/H₂) as well as chemoorganoheterotrophically in presence of various organic substrates. All pathways for synthesizing the 20 proteinogenic amino acids are present. In addition, two presumably complete gene sets for NADH:quinone oxidoreductase (complex I) were identified in the genome and there is evidence that either NADH or reduced ferredoxin might serve as electron donor. Beside the typical archaeal A₀A₁-ATP synthase, a membrane-bound pyrophosphatase is found, which might contribute to energy conservation. Surprisingly, all genes required for dissimilatory sulfate reduction are present, which is confirmed by growth experiments. Mentionable is furthermore, the presence of two proteins (ParA family ATPase, actin-like protein) that might be involved in cell division in Thermoproteales, where the ESCRT system is absent, and of genes involved in genetic competence (DprA, ComF) that is so far unique within Archaea.

• Haloquadratum walsbyi: limited diversity in a global pond.

  Authors: Mike L Dyall-Smith, Friedhelm Pfeiffer, Kathrin Klee, Peter Palm, Karin Gross, Stephan C Schuster, Markus Rampp, Dieter Oesterhelt

  PloS one. 01/2011; 6(6):e20968.

  Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit itsHaloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared. Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea. Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

• Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks.

  Authors: Giovanna Carpi, Francesca Cagnacci, Nicola E Wittekindt, Fangqing Zhao, Ji Qi, Lynn P Tomsho, Daniela I Drautz, Annapaola Rizzoli, Stephan C Schuster

  PloS one. 01/2011; 6(10):e25604.

  Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and forAssessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.

• Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.

  Authors: Charlotte Lindqvist, Stephan C Schuster, Yazhou Sun, Sandra L Talbot, Ji Qi, Aakrosh Ratan, Lynn P Tomsho, Lindsay Kasson, Eve Zeyl, Jon Aars, Webb Miller, Olafur Ingólfsson, Lutz Bachmann, Oystein Wiig

  Proceedings of the National Academy of Sciences of the United States of America. 03/2010; 107(11):5053-7.

  The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossilThe polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

• Calling SNPs without a reference sequence.

  Authors: Aakrosh Ratan, Yu Zhang, Vanessa M Hayes, Stephan C Schuster, Webb Miller

  BMC bioinformatics. 03/2010; 11:130.

  The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the sameThe most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies. We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences. DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/.

• Complete Khoisan and Bantu genomes from southern Africa.

  Authors: Stephan C Schuster, Webb Miller, Aakrosh Ratan, Lynn P Tomsho, Belinda Giardine, Lindsay R Kasson, Robert S Harris, Desiree C Petersen, Fangqing Zhao, Ji Qi [......] Elaine R Mardis, Nick Patterson, Tom H Pringle, Francesca Chiaromonte, James C Mullikin, Evan E Eichler, Ross C Hardison, Richard A Gibbs, Timothy T Harkins, Vanessa M Hayes

  Nature. 02/2010; 463(7283):943-7.

  The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based onThe genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

• Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation.

  Authors: Elizabeth A Tindall, Desiree C Petersen, Stina Nikolaysen, Webb Miller, Stephan C Schuster, Vanessa M Hayes

  BMC research notes. 02/2010; 3:39.

  High-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generationHigh-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generation sequencing (NGS) technologies. We investigate the Illumina GoldenGate chemistry using custom designed VeraCode and sentrix array matrix (SAM) assays for each of these applications, respectively. We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors. We illustrate the dramatic effect of outliers in genotype calling and data interpretation, as well as suggest simple means to avoid genotyping errors. Furthermore we present this platform as a successful method for two-cluster rare or non-autosomal variant calling. The success of high-throughput technologies to accurately call rare variants will become an essential feature for future association studies. Finally, we highlight additional advantages of the Illumina GoldenGate chemistry in generating unusually segregated cluster plots that identify potential NGS generated sequencing error resulting from minimal coverage. We demonstrate the importance of visually inspecting genotype cluster plots generated by the Illumina software and issue warnings regarding commonly accepted quality control parameters. In addition to suggesting applications to minimise data exclusion, we propose that the Illumina cluster plots may be helpful in identifying potential in-put sequence errors, particularly important for studies to validate NGS generated variation.

• Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.

  Authors: Webb Miller, Stephen J Wright, Yu Zhang, Stephan C Schuster, Vanessa M Hayes

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 01/2010;

  Methods from genetics and genomics can be employed to help save endangered species. One potential use is to provide a rational strategy for selecting a population of founders for a captive breedingMethods from genetics and genomics can be employed to help save endangered species. One potential use is to provide a rational strategy for selecting a population of founders for a captive breeding program. The hope is to capture most of the available genetic diversity that remains in the wild population, to provide a safe haven where representatives of the species can be bred, and eventually to release the progeny back into the wild. However, the founders are often selected based on a random-sampling strategy whose validity is based on unrealistic assumptions. Here we outline an approach that starts by using cutting-edge genome sequencing and genotyping technologies to objectively assess the available genetic diversity. We show how combinatorial optimization methods can be applied to these data to guide the selection of the founder population. In particular, we develop a mixed-integer linear programming technique that identifies a set of animals whose genetic profile is as close as possible to specified abundances of alleles (i.e., genetic variants), subject to constraints on the number of founders and their genders and ages.

• Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered Species.

  Authors: Webb Miller, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, Vanessa M. Hayes

  Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela, Hawaii, USA, 4-8 January 2010; 01/2010