Publications (54)528.13 Total impact
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Article: The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels
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ABSTRACT: BACKGROUND:The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.RESULTS:To build the N. furzeri transcript catalogue, thirteen cDNA libraries were sequenced using Sanger, 454/Roche and Solexa/Illumina technologies yielding about 39 Gb. In total, 19,875 protein-coding genes were identified and annotated. Of these, 71% are represented by at least one transcript contig with a complete coding sequence. Further, transcript levels of young and old fish of the strains GRZ and MZM-0403, which differ in lifespan by twofold, were studied by RNA-seq. In skin and brain, 85 differentially expressed genes were detected; these have a role in cell cycle coBMC Genomics 03/2013; 14(1):185. · 4.07 Impact Factor -
Article: Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.).
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ABSTRACT: Soil-borne barley yellow mosaic virus disease, caused by different strains of Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), is one of the most important diseases of winter barley (Hordeum vulgare L.) in Europe and East Asia. The recessive resistance gene rym11 located in the centromeric region of chromosome 4HL is effective against all so far known strains of BaMMV and BaYMV in Germany. In order to isolate this gene, a high-resolution mapping population (10,204 meiotic events) has been constructed. F2 plants were screened with co-dominant flanking markers and segmental recombinant inbred lines (RILs) were tested for resistance to BaMMV under growth chamber and field conditions. Tightly linked markers were developed by exploiting (1) publicly available barley EST sequences, (2) employing barley synteny to rice, Brachypodium distachyon and sorghum and (3) using next-generation sequencing data of barley. Using this approach, the genetic interval was efficiently narrowed down from the initial 10.72 % recombination to 0.074 % recombination. A marker co-segregating with rym11 was developed providing the basis for gene isolation and efficient marker-assisted selection.Theoretical and Applied Genetics 03/2013; · 3.30 Impact Factor -
Dataset: JNature12
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Article: Association studies of the copy-number variable Ss-defensin cluster on 8p23.1 in adenocarcinoma and chronic pancreatitis.
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ABSTRACT: BACKGROUND: Human Ss-defensins are a family of antimicrobial peptides located at the mucosal surface. Both sequence multi-site variations (MSV) and copy-number variants (CNV) of the defensin-encoding genes are associated with increased risk for various diseases, including cancer and inflammatory conditions such as psoriasis and acute pancreatitis. In a case--control study, we investigated the association between MSV in DEFB104 as well as defensin gene (DEF) cluster copy number (CN), and pancreatic ductal adenocarcinoma (PDAC) and chronic pancreatitis (CP). RESULTS: Two groups of PDAC (N=70) and CP (N=60) patients were compared to matched healthy control groups CARLA1 (N=232) and CARLA2 (N=160), respectively. Four DEFB104 MSV were haplotyped by PCR, cloning and sequencing. DEF cluster CN was determined by multiplex ligation-dependent probe amplification.Neither the PDAC nor the CP cohorts show significant differences in the DEFB104 haplotype distribution compared to the respective control groups CARLA1 and CARLA2, respectively.The diploid DEF cluster CN exhibit a significantly different distribution between PDAC and CARLA1 (Fisher's exact test P=0.027), but not between CP and CARLA2 (P=0.867). CONCLUSION: Different DEF cluster b CN distribution between PDAC patients and healthy controls indicate a potential protective effect of higher CNs against the disease.BMC Research Notes 11/2012; 5(1):629. -
Article: The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization.
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ABSTRACT: In higher plants the large-scale structure of monocentric chromosomes consists of distinguishable eu- and heterochromatic regions, the proportions and organization of which depend on a species' genome size. To find out whether the same interplay is maintained for holocentric chromosomes we investigated the distribution of repetitive sequences and epigenetic marks in the wood-rush Luzula elegans (3.81 Gbp/1C). Sixty-one per cent of the L. elegans genome is characterized by highly repetitive DNA, with over thirty distinct sequence families encoding an exceptionally high diversity of satellite repeats. Over 33% of the genome is composed of the Angela clade of Ty1/copia LTR-retrotransposons which are uniformly dispersed along the chromosomes, while the satellite repeats occur as bands whose distribution appears proportionally to be biased towards the chromosome termini. No satellite showed a distribution pattern that might be expected for the almost chromosome-wide distribution of the centromere, and no typical centromere-associated LTR-retrotransposons were found either. No distinguishable large-scale patterns of eu- and heterochromatin-typical epigenetic marks, or early/late DNA replicating domains were found along mitotic chromosomes, although super-high resolution light microscopy revealed distinguishable interspersed units of different chromatin types. Our data suggest a correlation between the centromere and overall genome organization in species with holocentric chromosomes. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.The Plant Journal 10/2012; · 6.16 Impact Factor -
Article: A physical, genetic and functional sequence assembly of the barley genome.
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ABSTRACT: Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.Nature 10/2012; · 36.28 Impact Factor -
Article: A physical, genetic and functional sequence assembly of the barley genome
Nature 10/2012; · 36.28 Impact Factor -
Article: A physical, genetic and functional sequence assembly of the barley genome
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ABSTRACT: A physical, genetic and functional sequence assembly of the barley genome The International Barley Genome Sequencing Consortium* Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement. Cultivated barley, derived from its wild progenitor Hordeum vulgare ssp. spontaneum, is among the world's earliest domesticated crop species 1 and today represents the fourth most abundant cereal in both area and tonnage harvested (http://faostat.fao.org). Approximately three-quarters of global production is used for animal feed, 20% is malted for use in alcoholic and non-alcoholic beverages, and 5% as an ingredient in a range of food products 2 . Barley is widely adapted to diverse environmental conditions and is more stress tolerant than its close relative wheat 3 . As a result, barley remains a major food source in poorer countries 4 , maintaining harvestable yields in harsh and marginal environments. In more developed societies it has recently been classified as a true functional food. Barley grain is particularly high in soluble dietary fibre, which significantly reduces the risk of serious human dis-eases including type II diabetes, cardiovascular disease and colorectal cancers that afflict hundreds of millions of people worldwide 5 . The USA Food and Drug Administration permit a human health claim for cell-wall polysaccharides from barley grain. As a diploid, inbreeding, temperate crop, barley has traditionally been considered a model for plant genetic research. Large collections of germplasm containing geographically diverse elite varieties, land-races and wild accessions are readily available 6 and undoubtedly con-tain alleles that could ameliorate the effect of climate change and further enhance dietary fibre in the grain. Enriching its broad natural diversity, extensive characterized mutant collections containing all of the morphological and developmental variation observed in the species have been generated, characterized and meticulously main-tained. The major impediment to the exploitation of these resources in fundamental and breeding science has been the absence of a reference genome sequence, or an appropriate enabling alternative. Providing either of these has been the primary research challenge to the global barley community. In response to this challenge, we present a novel model for deliver-ing the genome resources needed to reinforce the position of barley as a model for the Triticeae, the tribe that includes bread and durum wheats, barley and rye. We introduce the barley genome gene space, which we define as an integrated, multi-layered informational resource that provides access to the majority of barley genes in a highly structured physical and genetic framework. In association with comparative sequence and transcriptome data, the gene space provides a new molecular and cellular insight into the biology of the species, providing a platform to advance gene discovery and genome-assisted crop improvement.Nature 10/2012; · 36.28 Impact Factor -
Article: A physical, genetic and functional sequence assembly of the barley genome
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ABSTRACT: A physical, genetic and functional sequence assembly of the barley genome The International Barley Genome Sequencing Consortium* Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement. Cultivated barley, derived from its wild progenitor Hordeum vulgare ssp. spontaneum, is among the world's earliest domesticated crop species 1 and today represents the fourth most abundant cereal in both area and tonnage harvested (http://faostat.fao.org). Approximately three-quarters of global production is used for animal feed, 20% is malted for use in alcoholic and non-alcoholic beverages, and 5% as an ingredient in a range of food products 2 . Barley is widely adapted to diverse environmental conditions and is more stress tolerant than its close relative wheat 3 . As a result, barley remains a major food source in poorer countries 4 , maintaining harvestable yields in harsh and marginal environments. In more developed societies it has recently been classified as a true functional food. Barley grain is particularly high in soluble dietary fibre, which significantly reduces the risk of serious human dis-eases including type II diabetes, cardiovascular disease and colorectal cancers that afflict hundreds of millions of people worldwide 5 . The USA Food and Drug Administration permit a human health claim for cell-wall polysaccharides from barley grain. As a diploid, inbreeding, temperate crop, barley has traditionally been considered a model for plant genetic research. Large collections of germplasm containing geographically diverse elite varieties, land-races and wild accessions are readily available 6 and undoubtedly con-tain alleles that could ameliorate the effect of climate change and further enhance dietary fibre in the grain. Enriching its broad natural diversity, extensive characterized mutant collections containing all of the morphological and developmental variation observed in the species have been generated, characterized and meticulously main-tained. The major impediment to the exploitation of these resources in fundamental and breeding science has been the absence of a reference genome sequence, or an appropriate enabling alternative. Providing either of these has been the primary research challenge to the global barley community. In response to this challenge, we present a novel model for deliver-ing the genome resources needed to reinforce the position of barley as a model for the Triticeae, the tribe that includes bread and durum wheats, barley and rye. We introduce the barley genome gene space, which we define as an integrated, multi-layered informational resource that provides access to the majority of barley genes in a highly structured physical and genetic framework. In association with comparative sequence and transcriptome data, the gene space provides a new molecular and cellular insight into the biology of the species, providing a platform to advance gene discovery and genome-assisted crop improvement.Nature 10/2012; · 36.28 Impact Factor -
Article: Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae.
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ABSTRACT: Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ∼200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.PLoS ONE 01/2012; 7(9):e45307. · 4.09 Impact Factor -
Article: Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1.
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ABSTRACT: The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.PLoS ONE 01/2012; 7(2):e30784. · 4.09 Impact Factor -
Article: Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination.
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ABSTRACT: Genotyping of 21 varicella-zoster virus (VZV) strains using a scattered single nucleotide polymorphism (SNP) method revealed ambiguous SNPs and two nontypeable isolates. For a further genetic characterization, the genomes of all strains were sequenced using the 454 technology. Almost-complete genome sequences were assembled, and most remaining gaps were closed with Sanger sequencing. Phylogenetic analysis of 42 genomes revealed five established and two novel VZV genotypes, provisionally termed VIII and IX. Genotypes VIII and IX are distinct from the previously reported provisional genotypes VI and VII as judged from the SNP pattern. The alignments showed evidence of ancient recombination events in the phylogeny of clade 4 and recent recombinations within single strains: 3/2005 (clade 1), 11 and 405/2007 (clade 3), 8 and DR (clade 4), CA123 and 413/2000 (clade 5), and strains of the novel genotypes VIII and IX. Bayesian tree inference of the thymidine kinase and the polymerase genes of the VZV clades and other varicelloviruses revealed that VZV radiation began some 110,000 years ago, which correlates with the out-of-Africa dispersal of modern humans. The split of ancestral clades 2/4 and 1/3/5/VIII/IX shows the greatest node height.Journal of Virology 11/2011; 86(3):1608-22. · 5.40 Impact Factor -
Article: From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).
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ABSTRACT: The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.BMC Plant Biology 09/2011; 11:131. · 3.45 Impact Factor -
Article: Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae.
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ABSTRACT: The genomes of cereals such as wheat (Triticum aestivum) and barley (Hordeum vulgare) are large and therefore problematic for the map-based cloning of agronomicaly important traits. However, comparative approaches within the Poaceae permit transfer of molecular knowledge between species, despite their divergence from a common ancestor sixty million years ago. The finding that null variants of the rice gene cytokinin oxidase/dehydrogenase 2 (OsCKX2) result in large yield increases provides an opportunity to explore whether similar gains could be achieved in other Poaceae members. Here, phylogenetic, molecular and comparative analyses of CKX families in the sequenced grass species rice, brachypodium, sorghum, maize and foxtail millet, as well as members identified from the transcriptomes/genomes of wheat and barley, are presented. Phylogenetic analyses define four Poaceae CKX clades. Comparative analyses showed that CKX phylogenetic groupings can largely be explained by a combination of local gene duplication, and the whole-genome duplication event that predates their speciation. Full-length OsCKX2 homologues in barley (HvCKX2.1, HvCKX2.2) and wheat (TaCKX2.3, TaCKX2.4, TaCKX2.5) are characterized, with comparative analysis at the DNA, protein and genetic/physical map levels suggesting that true CKX2 orthologs have been identified. Furthermore, our analysis shows CKX2 genes in barley and wheat have undergone a Triticeae-specific gene-duplication event. Finally, by identifying ten of the eleven CKX genes predicted to be present in barley by comparative analyses, we show that next-generation sequencing approaches can efficiently determine the gene space of large-genome crops. Together, this work provides the foundation for future functional investigation of CKX family members within the Poaceae.Plant Biotechnology Journal 08/2011; 10(1):67-82. · 5.44 Impact Factor -
Article: A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome.
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ABSTRACT: Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.Functional & Integrative Genomics 08/2011; 11(4):671-7. · 3.83 Impact Factor -
Article: Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives.
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ABSTRACT: All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.The Plant Cell 05/2011; 23(5):1706-18. · 8.99 Impact Factor -
Article: Unlocking the barley genome by chromosomal and comparative genomics.
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ABSTRACT: We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.The Plant Cell 04/2011; 23(4):1249-63. · 8.99 Impact Factor -
Article: Highly parallel gene-to-BAC addressing using microarrays.
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ABSTRACT: Second-generation sequencing now provides the potential for low-cost generation of whole-genome sequences. However, for large-genome organisms with high repetitive DNA content, genome-wide short read sequence assembly is currently impossible, with accurate ordering and localization of genes still relying heavily on integration with physical and genetic maps. To facilitate this process, we have used Agilent microarrays to simultaneously address thousands of gene sequences to individual BAC clones and contiguous sequences that form part of an emerging physical map of the large and currently unsequenced 5.3-Gb barley genome. The approach represents a cost-effective, highly parallel alternative to traditional addressing methods. By coupling the gene-to-BAC address data with gene-based molecular markers, thousands of BACs can be anchored directly to the genetic map, thereby generating a framework for orientating and ordering genes, and providing direct links to phenotypic traits.BioTechniques 03/2011; 50(3):165-74. · 2.67 Impact Factor -
Article: Sequencing of BAC pools by different next generation sequencing platforms and strategies.
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ABSTRACT: ABSTRACT: Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library.Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.BMC Research Notes 01/2011; 4:411. -
Article: Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing.
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ABSTRACT: In highly copy number variable (CNV) regions such as the human defensin gene locus, comprehensive assessment of sequence variations is challenging. PCR approaches are practically restricted to tiny fractions, and next-generation sequencing (NGS) approaches of whole individual genomes e.g. by the 1000 Genomes Project is confined by an affordable sequence depth. Combining target enrichment with NGS may represent a feasible approach. As a proof of principle, we enriched a ~850 kb section comprising the CNV defensin gene cluster DEFB, the invariable DEFA part and 11 control regions from two genomes by sequence capture and sequenced it by 454 technology. 6,651 differences to the human reference genome were found. Comparison to HapMap genotypes revealed sensitivities and specificities in the range of 94% to 99% for the identification of variations.Using error probabilities for rigorous filtering revealed 2,886 unique single nucleotide variations (SNVs) including 358 putative novel ones. DEFB CN determinations by haplotype ratios were in agreement with alternative methods. Although currently labor extensive and having high costs, target enriched NGS provides a powerful tool for the comprehensive assessment of SNVs in highly polymorphic CNV regions of individual genomes. Furthermore, it reveals considerable amounts of putative novel variations and simultaneously allows CN estimation.BMC Genomics 01/2011; 12(1):243. · 4.07 Impact Factor
Top co-authors
Top Journals
- Nature (6)
- BMC Genomics (5)
- PLoS ONE (3)
- Human Mutation (2)
- The Plant Journal (2)
Institutions
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2009–2012
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Helmholtz Zentrum München
- Institut für Bioinformatik und Systembiologie
München, Bavaria, Germany -
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung
Gatersleben, Saxony-Anhalt, Germany
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2009–2011
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University of Zurich
Zürich, ZH, Switzerland
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2006–2011
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Leibniz Institute for Age Research - Fritz Lipmann Institute
- Genome Analysis
Jena, Thuringia, Germany
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2008–2010
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Rheinische Friedrich-Wilhelms-Universität Bonn
- Kekulé Institute of Organic Chemistry and Biochemistry
Bonn, North Rhine-Westphalia, Germany
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