The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

/pdf/phytozome-a-comparative-platform-for-green-plant-genomics-1ezqiu8w9i.pdf

Phytozome: a comparative platform for green plant genomics

Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.

/pdf/blast-ring-image-generator-brig-simple-prokaryote-genome-378atiw36f.pdf

BLAST Ring Image Generator (BRIG) : simple prokaryote genome comparisons

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

/pdf/the-genome-of-the-mesopolyploid-crop-species-brassica-rapa-54ka2hnfpp.pdf

The genome of the mesopolyploid crop species Brassica rapa

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

MOF-derived hierarchical porous carbon octahedrons for aluminum-ion batteries

Nucleotide sequence specific for O-antigen of E.coli 076 type

The invention provides a strain of Geobacillus thermodenitrificans as well as the screening method and the uses thereof. The strain was deposited as the number CGMCC-1228 in the China General Microbiological Culture Collection Center of the China Committee of Culture Collection for Microorganisms. The strain was obtained by primary screening, re-screening, inoculation, domestication and propagation using the bacteria in the aqueous samples from the strata of oil field as the original screening strain. The strain screened in the invention belongs to the genus Geobacillus , which can tolerate a high temperature, and has good thermostability, which can be applied to the industrial production which need the condition of thermostable enzymes, such as fermentation, etc. With its ability of growing well in the oil-reservoir environment, degrading alkanes, decreasing viscosity and increasing fluidity of crude oil, the strain is able to remarkably enhance the yield of oil and improve the transporting efficiency of oil. Additionally, with its good ability of degrading oil, it can be developed for the treatment and clearing of the material such as the oil contaminated water, etc., so it can be useful in protection of the environment. This strain also has the ability of decreasing the surface tension of substances, which can be applied to the industry of biosurfactants preparation.

Geobacillus thermodenitrificans as well as the screening method and the uses thereof

The present invention provides a kind of nucleotide specific to O-antigen of Escherichia coli O71, and it is the total nucleotide sequence of gene cluster of Escherichia coli O71 to control the synthesis of O-antigen, such as separated nucleotide shown in SEQ ID No. 1 with whole length of 13743 bases; nucleotide similar to that in SEQ ID No. 1 with one or several inserted, deleted or substituted bases; and oligonucleotide originated glycosyltransferase gene and oligose unit processing gene of Escherichia coli O71 antigen gene cluster. PCR proves the high specificity of the oligonucleotide on the Escherichia coli O71 antigen. The present invention also discloses the method of detecting and identifying the Escherichia coli O71 in human body and in environment with the oligonucleotide of the present invention.

O-antigen specific nucleotide of E.coli 071 type

Sulfoxaflor adversely influences the biological characteristics of Coccinella septempunctata by suppressing vitellogenin expression and predation activity.

Lei Wang

Papers

MOF-derived hierarchical porous carbon octahedrons for aluminum-ion batteries

Nucleotide sequence specific for O-antigen of E.coli 076 type

Geobacillus thermodenitrificans as well as the screening method and the uses thereof

O-antigen specific nucleotide of E.coli 071 type

Sulfoxaflor adversely influences the biological characteristics of Coccinella septempunctata by suppressing vitellogenin expression and predation activity.