ArticleBMC genomics2009
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Peripheral pulmonary nodule diagnosed as mycobacterium chelonae using electromagnetic navigation bronchoscopy combined with next generation sequencing: a case report.American journal of translational research · 2020Article
- Second-Generation Sequencing with Deep Reinforcement Learning for Lung Infection Detection.Journal of healthcare engineering · 2020Article
- The Challenge of Analyzing the Sugarcane Genome.Frontiers in plant science · 2018Review
- Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.Scientific data · 2017Article
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- EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis.Nucleic acids research · 2016Article
- Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes.Plant biotechnology journal · 2016Article
- The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning.Plant physiology · 2015Article
- Complete nucleotide sequence of Klebsiella phage P13 and prediction of an EPS depolymerase gene.Virus genes · 2015Article
- Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels.Frontiers in bioengineering and biotechnology · 2015Review
- Bovine serum albumin in saliva mediates grazing response in Leymus chinensis revealed by RNA sequencing.BMC genomics · 2014Article
- The barley Frost resistance-H2 locus.Functional & integrative genomics · 2014Article
- A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.Plant physiology · 2014Article
- BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower.BMC genomics · 2013Article
- Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.).BMC genomics · 2013Article
- Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.PloS one · 2013Article
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13 authors.
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Abstract
backgroundDe novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L.) is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable.
resultsTo test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of approximately 50 kb (N80 approximately 31 kb, N90 approximately 21 kb) and a Q40 of 94%. For approximately 80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes.By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies.
conclusionThe described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.
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