Simultaneous alignment of short reads against multiple genomes

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.     

Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T

Halogranum salarium is an extremely halophilic archaeon isolated from evaporitic salt crystals and belongs to the family Halobacteriaceae. Here, we present the 4.5-Mb draft genome sequence of the type strain (B-1^T) of H. salarium. This is the first report of the draft genome sequence of a haloarchaeon in the genus Halogranum.     

An improved genome reference for the African cichlid,Metriaclima zebra

Background

Problems associated with using draft genome assemblies are well documented and have become more pronounced with the use of short read data for de novo genome assembly. We set out to improve the draft genome assembly of the African cichlid fish, Metriaclima zebra, using a set of Pacific Biosciences SMRT sequencing reads corresponding to 16.5× coverage of the genome. Here we characterize the improvements that these long reads allowed us to make to the state-of-the-art draft genome previously assembled from short read data.

Results

Our new assembly closed 68 % of the existing gaps and added 90.6Mbp of new non-gap sequence to the existing draft assembly of M. zebra. Comparison of the new assembly to the sequence of several bacterial artificial chromosome clones confirmed the accuracy of the new assembly. The closure of sequence gaps revealed thousands of new exons, allowing significant improvement in gene models. We corrected one known misassembly, and identified and fixed other likely misassemblies. 63.5 Mbp (70 %) of the new sequence was classified as repetitive and the new sequence allowed for the assembly of many more transposable elements.

Conclusions

Our improvements to the M. zebra draft genome suggest that a reasonable investment in long reads could greatly improve many comparable vertebrate draft genome assemblies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1930-5) contains supplementary material, which is available to authorized users.     

Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43

This work describes the draft genome sequence of Lactococcus garvieae DCC43. The 2.2-Mb draft genome contains 2,227 predicted protein-coding genes, among which is a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or capsule-related virulence genes were identified. Two plasmid replication regions indicate that this strain likely contains plasmids. Comparative genomics suggests that this strain displays a high degree of sequence variation from the previously sequenced L. garvieae strains.     

Draft Genome Sequence of Staphylococcus vitulinus F1028, a Strain Isolated from a Block of Fermented Soybean

Staphylococcus vitulinus is a coagulase-negative staphylococcus in the family Staphylococcaceae. This report describes the draft genome sequence of S. vitulinus F1028, which was isolated from a traditional Korean soybean food (meju). This 2.56-Mbp genome sequence is the first S. vitulinus genome of a strain isolated from a fermented soybean product.     

Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1

Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we report the draft genome sequence of E. coli AI27. This is the first porcine strain in the phylogenetic group B1 whose genome sequence has been determined.     

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

We report here the 6.97-Mb draft genome sequence of Pseudomonas fluorescens strain NCIMB 11764, which is capable of growth on cyanide as the sole nitrogen source. The draft genome sequence allowed the discovery of several genes implicated in enzymatic cyanide turnover and provided additional information contributing to a better understanding of this organism''s unique cyanotrophic ability. This is the first sequenced genome of a cyanide-assimilating bacterium.     

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida S11

Here we report the genome sequence of a plant growth-promoting rhizobacterium, Pseudomonas putida S11. The length of the draft genome sequence is approximately 5,970,799 bp, with a G+C content of 62.4%. The genome contains 6,076 protein-coding sequences.     

Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones,Isolated from Malaysian Tropical Soil

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.     

Genome Sequence of Lactobacillus ingluviei,a Bacterium Associated with Weight Gain in Animals

We report the draft genome sequence of Lactobacillus ingluviei strain Autruche 4 (CSURP209) isolated from an ostrich. L. ingluviei is associated with weight gain in mice. This genome sequence may help us understand the obesity-induced mechanisms of intestinal bacteria.     

The draft genome sequence of the nematode <Emphasis Type="Italic">Caenorhabditis briggsae</Emphasis>, a companion to <Emphasis Type="Italic">C. elegans</Emphasis>

The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of its close relative Caenorhabditis elegans and will facilitate comparative genomics and the study of the evolutionary changes during development.     

Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp. Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation

We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades quorum-sensing molecules (namely, N-acyl homoserine lactones). To the best of our knowledge, this is the first documentation that reports the whole genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.     

Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056

Pseudomonas aeruginosa is an important cause of disease in hospitalized and immunocompromised patients. The genome of P. aeruginosa is among the largest of bacteria pathogenic to humans. We present the draft genome sequence of P. aeruginosa strain PABL056, a human bloodstream isolate with the largest genome yet reported in P. aeruginosa.     

Draft Genome Sequence of Bacillus anthracis UR-1, Isolated from a German Heroin User

We report the draft genome sequence of Bacillus anthracis UR-1, isolated from a fatal case of injectional anthrax in a German heroin user. Analysis of the genome sequence of strain UR-1 may aid in describing phylogenetic relationships between virulent heroin-associated isolates of B. anthracis isolated in the United Kingdom, Germany, and other European countries.     

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.     

Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier

We report the draft genome sequence of Paenisporosarcina sp. strain TG-20, which is 4.12 Mb in size and consists of 4,071 protein-coding genes and 76 RNA genes. The genome sequence of Paenisporosarcina sp. TG-20 may provide useful information about molecular adaptations that enhance survival in icy subsurface environments.     

Draft Genome Sequence of CBS 2479, the Standard Type Strain of Trichosporon asahii

Trichosporon asahii is one of the important opportunistic pathogenic fungi. Here, we first report the draft nuclear chromosome genome sequence and mitochondrial genome sequence of T. asahii CBS 2479, which is a standard strain of T. asahii that was isolated from a progressive psoriatic lesion. COG analysis predicted that 3,131 genes were assigned to 23 functional categories and that 628 genes were predicted to have a general function.     

Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes

The publication of the Fugu rubripes draft genome sequence will take this fish from culinary delicacy to potent tool in deciphering the mysteries of human genome function.     

Draft Genome Sequence of Actinobacillus pleuropneumoniae Serotype 7 Strain S-8

The Gram-negative bacterium Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease that leads to severe economic losses in the swine industry. For years, scientists working with it have lacked a reliable genome sequence for comparison with other Actinobacillus species. Here, we report the draft genome sequence of A. pleuropneumoniae serotype 7 (strain S-8), isolated from swine lung in China in 1992.     

Genome Sequence of Acinetobacter baumannii AC12, a Polymyxin-Resistant Strain Isolated from Terengganu,Malaysia

Acinetobacter baumannii is a major cause of nosocomial infection worldwide. We report the draft genome sequence of A. baumannii AC12, a multidrug-resistant nosocomial strain with additional resistance to carbapenems and polymyxin. The genome data will provide insights into the genetic basis of antimicrobial resistance and its adaptive mechanism.