Ji Qi

Publications of Ji Qi

• Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis.

  Authors: Pingli Lu, Xinwei Han, Ji Qi, Jiange Yang, Asela J Wijeratne, Tao Li, Hong Ma

  Genome research. 11/2011; 22(3):508-18.

  Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributingMeiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 443 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enrichment for disease-resistance genes. Another 316 genes are affected by large indels, including 130 genes with complete deletion of coding regions in Ler. Using the Arabidopsis qrt1 mutant, two sets of four meiotic products were generated and analyzed by sequencing for meiotic recombination, representing the first tetrad analysis with whole-genome sequencing in a nonfungal species. We detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed genome variation in meiotic products, contributing to population diversity. In particular, meiosis provides a rapid mechanism to generate copy-number variation (CNV) of sequences that have different chromosomal positions in Col and Ler.

• inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data.

  Authors: Ji Qi, Fangqing Zhao

  Nucleic acids research. 07/2011; 39(Web Server issue):W567-75.

  Mining genetic variation from personal genomes is a crucial step towards investigating the relationship between genotype and phenotype. However, compared to the detection of SNPs and small indels,Mining genetic variation from personal genomes is a crucial step towards investigating the relationship between genotype and phenotype. However, compared to the detection of SNPs and small indels, characterizing large and particularly complex structural variation is much more difficult and less intuitive. In this article, we present a new scheme (inGAP-sv) to detect and visualize structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important features, including local depth of coverage, mapping quality and associated tandem repeat, are used to evaluate the quality of predicted structural variation. Compared with other approaches, it can detect many more large insertions and complex variants with lower false discovery rate. Moreover, inGAP-sv, written in Java programming language, provides a user-friendly interface and can be performed in multiple operating systems. It can be freely accessed at http://ingap.sourceforge.net/.

• 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.

• 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.

• 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.

• Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics.

  Authors: Nicola E Wittekindt, Abinash Padhi, Stephan C Schuster, Ji Qi, Fangqing Zhao, Lynn P Tomsho, Lindsay R Kasson, Michael Packard, Paul Cross, Mary Poss

  PloS one. 01/2010; 5(10):e13432.

  The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches areThe ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.

• inGAP: an integrated next-generation genome analysis pipeline.

  Authors: Ji Qi, Fangqing Zhao, Anne Buboltz, Stephan C Schuster

  Bioinformatics (Oxford, England). 10/2009;

  SUMMARY: We develop a novel mining pipeline, inGAP, guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughputSUMMARY: We develop a novel mining pipeline, inGAP, guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly. AVAILABILITY: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap CONTACT: scs@bx.psu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius.

  Authors: Fangqing Zhao, Ji Qi, Stephan C Schuster

  Genome research. 07/2009;

  The woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial andThe woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial and nuclear genomes of this extinct species. Mammoths belong to Afrotheria, a group of mammals exhibiting extreme morphological diversity and large genome sizes. In this study, we found that the mammoth genome contains a larger proportion of interspersed repeats than any other mammalian genome reported so far, in which the proliferation of the RTE family of retrotransposons (covering 12% of the genome) may be the main reason for an increased genome size. Phylogenetic analysis showed that RTEs in mammoth are closely related to the family BovB/RTE. The incongruence of the reconstructed RTE phylogeny indicates that RTEs in mammoth may be acquired through an ancient lateral gene transfer event. A recent proliferation of SINEs was also found in the probocidean lineage, whereas the Afrotherian-wide SINEs in mammoth have undergone a rather flat and stepwise expansion. Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages.

• The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

  Authors: Webb Miller, Daniela I Drautz, Jan E Janecka, Arthur M Lesk, Aakrosh Ratan, Lynn P Tomsho, Mike Packard, Yeting Zhang, Lindsay R. McClellan, Ji Qi, Fangqing Zhao, M Thomas P Gilbert, Love Dalén, Juan Luis Arsuaga, Per G P Ericson, Daniel H Huson, Kristofer M. Helgen, William J Murphy, Anders Götherström, Stephan C Schuster

  Genome research. 02/2009;

  We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic positionWe report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

• Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae.

  Authors: Ji Qi, Asela J Wijeratne, Lynn P Tomsho, Yi Hu, Stephan C Schuster, Hong Ma

  BMC genomics. 01/2009; 10:475.

  BACKGROUND: Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loops formBACKGROUND: Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loops form either crossovers (COs) or non-crossovers (NCOs), which occur at many sites in the genome. Differences at the nucleotide level associated with COs and NCOs enable us to detect these recombination events and their distributions. RESULTS: We used high throughput sequencing to uncover over 46 thousand single nucleotide polymorphisms (SNPs) between two budding yeast strains and investigated meiotic recombinational events. We provided a detailed analysis of CO and NCO events, including number, size range, and distribution on chromosomes. We have detected 91 COs, very close to the average number from previous genetic studies, as well as 21 NCO events and mapped the positions of these events with high resolution. We have obtained DNA sequence-level evidence for a wide range of sizes of chromosomal regions involved in CO and NCO events. We show that a large fraction of the COs are accompanied by gene conversion (GC), indicating that meiotic recombination changes allelic frequencies, in addition to redistributing existing genetic variations. CONCLUSION: This work is the first reported study of meiotic recombination using high throughput sequencing technologies. Our results show that high-throughput sequencing is a sensitive method to uncover at single-base resolution details of CO and NCO events, including some complex patterns, providing new clues about the mechanism of this fundamental process.

• Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

  Authors: Ji Qi, Asela Wijeratne, Lynn Tomsho, Yi Hu, Stephan Schuster, Hong Ma

  BMC Genomics. 01/2009;

  Abstract Background Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loopsAbstract Background Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loops form either crossovers (COs) or non-crossovers (NCOs), which occur at many sites in the genome. Differences at the nucleotide level associated with COs and NCOs enable us to detect these recombination events and their distributions. Results We used high throughput sequencing to uncover over 46 thousand single nucleotide polymorphisms (SNPs) between two budding yeast strains and investigated meiotic recombinational events. We provided a detailed analysis of CO and NCO events, including number, size range, and distribution on chromosomes. We have detected 91 COs, very close to the average number from previous genetic studies, as well as 21 NCO events and mapped the positions of these events with high resolution. We have obtained DNA sequence-level evidence for a wide range of sizes of chromosomal regions involved in CO and NCO events. We show that a large fraction of the COs are accompanied by gene conversion (GC), indicating that meiotic recombination changes allelic frequencies, in addition to redistributing existing genetic variations. Conclusion This work is the first reported study of meiotic recombination using high throughput sequencing technologies. Our results show that high-throughput sequencing is a sensitive method to uncover at single-base resolution details of CO and NCO events, including some complex patterns, providing new clues about the mechanism of this fundamental process.

• Sequencing the nuclear genome of the extinct woolly mammoth.

  Authors: Webb Miller, Daniela I Drautz, Aakrosh Ratan, Barbara Pusey, Ji Qi, Arthur M Lesk, Lynn P Tomsho, Michael D Packard, Fangqing Zhao, Andrei Sher [......] Nick Patterson, Kerstin Lindblad-Toh, Eric S Lander, James R Knight, Gerard P Irzyk, Karin M Fredrikson, Timothy T Harkins, Sharon Sheridan, Tom Pringle, Stephan C Schuster

  Nature. 12/2008; 456(7220):387-90.

  In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number ofIn 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged, and studies to date have typically focused on short mitochondrial sequences, never yielding more than a fraction of a per cent of any nuclear genome. Here we describe 4.17 billion bases (Gb) of sequence from several mammoth specimens, 3.3 billion (80%) of which are from the woolly mammoth (Mammuthus primigenius) genome and thus comprise an extensive set of genome-wide sequence from an extinct species. Our data support earlier reports that elephantid genomes exceed 4 Gb. The estimated divergence rate between mammoth and African elephant is half of that between human and chimpanzee. The observed number of nucleotide differences between two particular mammoths was approximately one-eighth of that between one of them and the African elephant, corresponding to a separation between the mammoths of 1.5-2.0 Myr. The estimated probability that orthologous elephant and mammoth amino acids differ is 0.002, corresponding to about one residue per protein. Differences were discovered between mammoth and African elephant in amino-acid positions that are otherwise invariant over several billion years of combined mammalian evolution. This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.

• A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

  Authors: Travis N Mavrich, Ilya P Ioshikhes, Bryan J Venters, Cizhong Jiang, Lynn P Tomsho, Ji Qi, Stephan C Schuster, Istvan Albert, B Franklin Pugh

  Genome research. 07/2008; 18(7):1073-83.

  Most nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified byMost nucleosomes are well-organized at the 5' ends of S. cerevisiae genes where "-1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the -1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3' NFR that is present at >95% of all genes. 3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping.

• Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.

  Authors: M Thomas P Gilbert, Daniela I Drautz, Arthur M Lesk, Simon Y W Ho, Ji Qi, Aakrosh Ratan, Chih-Hao Hsu, Andrei Sher, Love Dalén, Anders Götherström [......] Vladimir Nikolaev, Malgosia Nowak-Kemp, James R Knight, Gerard P Irzyk, Clotilde S Perbost, Karin M Fredrikson, Timothy T Harkins, Sharon Sheridan, Webb Miller, Stephan C Schuster

  Proceedings of the National Academy of Sciences of the United States of America. 07/2008; 105(24):8327-32.

  We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material.We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

• Nucleosome organization in the Drosophila genome.

  Authors: Travis N Mavrich, Cizhong Jiang, Ilya P Ioshikhes, Xiaoyong Li, Bryan J Venters, Sara J Zanton, Lynn P Tomsho, Ji Qi, Robert L Glaser, Stephan C Schuster, David S Gilmour, Istvan Albert, B Franklin Pugh

  Nature. 06/2008; 453(7193):358-62.

  Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolutionComparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

• Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.

  Authors: Tim Urich, Anders Lanzén, Ji Qi, Daniel H Huson, Christa Schleper, Stephan C Schuster

  PLoS ONE. 02/2008; 3(6):e2527.

  BACKGROUND: Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soilBACKGROUND: Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification. METHODOLOGY/PRINCIPAL FINDINGS: Here we apply an RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community. Total community RNA is random reversely transcribed into cDNA without any PCR or cloning step. Direct pyrosequencing produces large numbers of cDNA rRNA-tags; these are taxonomically profiled in a binning approach using the MEGAN software and two specifically compiled rRNA reference databases containing small and large subunit rRNA sequences. The pyrosequencing also produces mRNA-tags; these provide a sequence-based transcriptome of the community. One soil dataset of 258,411 RNA-tags of approximately 98 bp length contained 193,219 rRNA-tags with valid taxonomic information, together with 21,133 mRNA-tags. Quantitative information about the relative abundance of organisms from all three domains of life and from different trophic levels was obtained in a single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identified by more than 2,000 rRNA-tags; furthermore, their activity in situ was revealed through the presence of mRNA-tags specific for enzymes involved in ammonia oxidation and CO(2) fixation. CONCLUSIONS/SIGNIFICANCE: This approach could be widely applied in microbial ecology by efficiently linking community structure and function in a single experiment while avoiding biases inherent in other methods.

• Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

  Authors: Istvan Albert, Travis N Mavrich, Lynn P Tomsho, Ji Qi, Sara J Zanton, Stephan C Schuster, B Franklin Pugh

  Nature. 04/2007; 446(7135):572-6.

  The nucleosome is the fundamental building block of eukaryotic chromosomes. Access to genetic information encoded in chromosomes is dependent on the position of nucleosomes along the DNA. AlternativeThe nucleosome is the fundamental building block of eukaryotic chromosomes. Access to genetic information encoded in chromosomes is dependent on the position of nucleosomes along the DNA. Alternative locations just a few nucleotides apart can have profound effects on gene expression. Yet the nucleosomal context in which chromosomal and gene regulatory elements reside remains ill-defined on a genomic scale. Here we sequence the DNA of 322,000 individual Saccharomyces cerevisiae nucleosomes, containing the histone variant H2A.Z, to provide a comprehensive map of H2A.Z nucleosomes in functionally important regions. With a median 4-base-pair resolution, we identify new and established signatures of nucleosome positioning. A single predominant rotational setting and multiple translational settings are evident. Chromosomal elements, ranging from telomeres to centromeres and transcriptional units, are found to possess characteristic nucleosomal architecture that may be important for their function. Promoter regulatory elements, including transcription factor binding sites and transcriptional start sites, show topological relationships with nucleosomes, such that transcription factor binding sites tend to be rotationally exposed on the nucleosome surface near its border. Transcriptional start sites tended to reside about one helical turn inside the nucleosome border. These findings reveal an intimate relationship between chromatin architecture and the underlying DNA sequence it regulates.

• MEGAN analysis of metagenomic data.

  Authors: Daniel H Huson, Alexander F Auch, Ji Qi, Stephan C Schuster

  Genome research. 04/2007; 17(3):377-86.

  Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role ofMetagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.

• Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

  Authors: Hendrik N. Poinar, Carsten Schwarz, Ji Qi, Beth Shapiro, Ross D E Macphee, Bernard Buigues, Alexei Tikhonov, Daniel H Huson, Lynn P Tomsho, Alexander Auch, Markus Rampp, Webb Miller, Stephan C Schuster

  Science (New York, N.Y.). 02/2006; 311(5759):392-4.

  We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use ofWe sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.