共查询到20条相似文献,搜索用时 31 毫秒
1.
Young-Do Nam Won-Hyong Chung Myung-Ji Seo Seong-Il Lim Sung-Hun Yi 《Journal of bacteriology》2012,194(21):5987
This report describes the draft genome sequence of Staphylococcus lentus F1142, which was isolated from a Korean fermented soybean paste (doenjang). The draft genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first S. lentus genome to be reported. 相似文献
2.
Korbinian Schneeberger Jörg Hagmann Stephan Ossowski Norman Warthmann Sandra Gesing Oliver Kohlbacher Detlef Weigel 《Genome biology》2009,10(9):1-12
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. 相似文献
3.
Daren C. Card Drew R. Schield Jacobo Reyes-Velasco Matthew K. Fujita Audra L. Andrew Sara J. Oyler-McCance Jennifer A. Fike Diana F. Tomback Robert P. Ruggiero Todd A. Castoe 《PloS one》2014,9(9)
As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark''s Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies. 相似文献
4.
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-1T) of H. salarium. This is the first report of the draft genome sequence of a haloarchaeon in the genus Halogranum. 相似文献
5.
Christina Gabrielsen Dag A. Brede Pablo E. Hernández Ingolf F. Nes Dzung B. Diep 《Journal of bacteriology》2012,194(24):6976-6977
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. 相似文献
6.
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. 相似文献7.
Paramasivan Ponraj Manoharan Shankar Devaraj Ilakkiam Jeyaprakash Rajendhran Paramasamy Gunasekaran 《Journal of bacteriology》2012,194(21):6015
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. 相似文献
8.
Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1
Kihyun Lee Hana Yi Yong-Joon Cho Jeonghwan Jang Hor-Gil Hur Jongsik Chun 《Journal of bacteriology》2012,194(23):6640-6641
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. 相似文献
9.
Guohong Liu Bo Liu Naiquan Lin Weiqi Tang Jianyang Tang Yingzhi Lin 《Journal of bacteriology》2012,194(23):6633
Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin''s Terracotta Warriors in Xi''an City, People''s Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%. 相似文献
10.
Young-Do Nam Won-Hyong Chung Myung-Ji Seo Seong-Il Lim 《Journal of bacteriology》2012,194(21):5961-5962
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. 相似文献
11.
Vicky Merhej Fabrice Armougom Catherine Robert Didier Raoult 《Journal of bacteriology》2012,194(20):5697
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. 相似文献
12.
Aurore Gorlas Grégory Gimenez Didier Raoult Véronique Roux 《Journal of bacteriology》2012,194(23):6613-6614
A draft genome sequence of Actinomyces timonensis, an anaerobic bacterium isolated from a human clinical osteoarticular sample, is described here. CRISPR-associated proteins, insertion sequence, and toxin-antitoxin loci were found on the genome. A new virus or provirus, AT-1, was characterized. 相似文献
13.
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. 相似文献
14.
Teik-Min Chong Hun-Jiat Tung Wai-Fong Yin Kok-Gan Chan 《Journal of bacteriology》2012,194(23):6611-6612
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. 相似文献
15.
Jun Hyuck Lee Hye Yeon Koh Sung Gu Lee Shawn Doyle Brent C. Christner Hak Jun Kim 《Journal of bacteriology》2012,194(23):6636
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. 相似文献
16.
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. 相似文献
17.
Kevin M. Dorn Johnathon D. Fankhauser Donald L. Wyse M. David Marks 《DNA research》2015,22(2):121-131
Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress. 相似文献
18.
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. 相似文献
19.
Christian Rückert Katharina Licht J?rn Kalinowski Christophe Espírito Santo Markus Antwerpen Matthias Hanczaruk Udo Reischl Thomas Holzmann André Gessner Carsten Tiemann Gregor Grass 《Journal of bacteriology》2012,194(21):5997-5998
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. 相似文献
20.
Rong Ya Yang Hai Tao Li He Zhu Guang Peng Zhou Meng Wang Lei Wang 《Eukaryotic cell》2012,11(11):1415-1416
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. 相似文献