Finding novel genes in bacterial communities isolated from the environment

Krause, Lutz; Diaz, Naryttza N.; Bartels, Daniela; Edwards, Robert A.; Pühler, Alfred; Rohwer, Forest; Meyer, Patrick; Stoye, Jens

doi:10.1093/bioinformatics/btl247

Cited by 69 publications

(34 citation statements)

References 21 publications

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“…Newbler (roche-applied-science.com) is distributed with 454 Life Sciences instruments and has been successfully used in the assembly of bacteria [20]. With sufficiently deep coverage, typically 25-30 times, the resulting assemblies are comparable to those obtained through Sanger sequencing [21]. Note, however, that these results do not account for the additional information provided by mate-pairs -information commonly available in Sanger data but only recently introduced to the 454 technology.…”

Section: De Novo Assemblymentioning

confidence: 99%

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The impact of next-generation sequencing technology on genetics

2008

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New DNA sequencing technologies can sequence up to one billion bases in a single day at low cost, putting large-scale sequencing within the reach of many scientists. Many researchers are forging ahead with projects to sequence a range of species using the new technologies. However, these new technologies produce read lengths as short as 35-40 nucleotides, posing challenges for genome assembly and annotation. Here we review the challenges and describe some of the bioinformatics systems that are being proposed to solve them. We specifically address issues arising from using these technologies in assembly projects, both de novo and for resequencing purposes, as well as efforts to improve genome annotation in the fragmented assemblies produced by short read lengths. New technologies: more data and new types of dataThe ongoing revolution in sequencing technology has led to the production of sequencing machines with dramatically lower costs and higher throughput than the technology of just 2 years ago. Sequencers from 454 Life Sciences/Roche, Solexa/Illumina and Applied Biosystems (SOLiD technology) are already in production, and a competing technology from Helicos should appear soon. However, the increase in the volume of raw sequence that can be produced from these sequencers is threatening to swamp our available data archives, because genomics centers are gearing up to produce much more data in the next several years. For example, major National Institutes of Health (NIH) sequencing centers are planning to sequence 100 complete human genomes in the next 2-3 years [1]. Furthermore, the increased throughput of the new sequencing machines makes it possible for biologists to sequence large numbers of bacterial strains and isolates, leading some microbiologists to suggest that we characterize the genomes of all organisms present in culture collections.These technologies greatly increase sequencing throughput by laying out millions of DNA fragments on a single chip and sequencing all these fragments in parallel. The various technologies differ in the procedures used to array the DNA fragments: 454 and Applied Biosystems first attach the DNA to coated beads, whereas Solexa and Helicos attach the DNA directly to the chip. (For a more detailed description of these technologies, see the companion article by Mardis [2].)

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Section: De Novo Assemblymentioning

confidence: 99%

“…In another recent development, Krause et al [21] enhanced a translated BLAST approach in an effort to make it more robust to the sequencing errors common in SRS projects. Their CARMA systems combines translated BLAST searches with a postprocessing step that merges protein fragments across frameshifts.…”

Section: Annotation Of Metagenomics Projectsmentioning

confidence: 99%

The impact of next-generation sequencing technology on genetics

2008

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“…Finally mass sequencing 30,85,187) or 16S rRNA mass cataloging 72) or even different methods 1,52,188) are appearing. Massive Parallel Sequencing (MPS) 4,56,110) that can presently produce 400,000 reads per run, with lengths averaging 200 to 300 bases per read (more than 20 million bases per 4.5-hour instrument run) now allows to sequence the entire molecule 161) or selectively variable short domains of the 16S rRNA gene 30,33,63,89,93,116,138,151,160,169) seemingly with good accuracy 70) . These short sequences will be referenced as "tags" below in this manuscript.…”

Section: Introductionmentioning

confidence: 99%

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen

2008

Microb. Environ.

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Roughly estimating the diversity of life has for a long time been seen as a challenge. Sequences obtained from the environment by direct amplification are now seen as the sole mean to provide information for at least 99% of the prokaryotes in natural communities. Recent massive parallel sequencing technologies now allow to sequence nearly every sequence resulting from such amplification. Are we ready to deal with such a deluge of data? Using three recent publications (16S rRNA genes amplification in soil and seawater followed by massive parallel sequencing) as case examples, this review analyses the state of the field.

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“…This new sequencer has been used to sequence bacterial genomes (Goldberg et al 2006), cDNAs (Ng et al 2006), small RNAs (Girard et al 2006), PCR products for whole genome surveys ) and for sequencing ancient DNA (Green et al 2006;Poinar et al 2006). In addition, the large sequence depth that can be obtained with micro-bead sequencing has made it possible to conduct a number of new metagenomic projects (Angly et al 2006;Edwards et al 2006;Krause et al 2006;Leininger et al 2006;Sogin et al 2006;Turnbaugh et al 2006). To date, a few publications have used this micro-bead sequencing platform for large-scale single nucleotide polymorphism (SNP) or structural variation discovery in animals (Korbel et al 2007;Malhi et al 2007) and for mutation discovery in cancer cells ; however, these approaches have relied upon a completed reference genomes for sequence comparison.…”

Section: Introductionmentioning

confidence: 99%

Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing

et al. 2008

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Heterodera glycines, the soybean cyst nematode (SCN), is a damaging agricultural pest that could be effectively managed if critical phenotypes, such as virulence and host range could be understood. While SCN is amenable to genetic analysis, lack of DNA sequence data prevents the use of such methods to study this pathogen. Fortunately, new methods of DNA sequencing that produced large amounts of data and permit whole genome comparative analyses have become available. In this study, 400 million bases of genomic DNA sequence were collected from two inbred biotypes of SCN using 454 micro-bead DNA sequencing. Comparisons to a BAC, sequenced by Sanger sequencing, showed that the micro-bead sequences could identify low and high copy number regions within the BAC. Potential single nucleotide polymorphisms (SNPs) between the two SCN biotypes were identified by comparing the two sets of sequences. Selected resequencing revealed that up to 84% of the SNPs were correct. We conclude that the quality of the micro-bead sequence data was sufficient for de novo SNP identification and should be applicable to organisms with similar genome sizes and complexities. The SNPs identified will be an important starting point in associating phenotypes with specific regions of the SCN genome.

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Finding novel genes in bacterial communities isolated from the environment

Abstract: The program is freely available upon request.

Cited by 69 publications

References 21 publications

The impact of next-generation sequencing technology on genetics

The impact of next-generation sequencing technology on genetics

Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing

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