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)

Targeted genome editing using engineered nucleases has rapidly gone from being a niche technology to a mainstream method used by many biological researchers. This widespread adoption has been largely fueled by the emergence of the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology, an important new approach for generating RNA-guided nucleases, such as Cas9, with customizable specificities. Genome editing mediated by these nucleases has been used to rapidly, easily and efficiently modify endogenous genes in a wide variety of biomedically important cell types and in organisms that have traditionally been challenging to manipulate genetically. Furthermore, a modified version of the CRISPR-Cas9 system has been developed to recruit heterologous domains that can regulate endogenous gene expression or label specific genomic loci in living cells. Although the genome-wide specificities of CRISPR-Cas9 systems remain to be fully defined, the power of these systems to perform targeted, highly efficient alterations of genome sequence and gene expression will undoubtedly transform biological research and spur the development of novel molecular therapeutics for human disease.

http://stacks.cdc.gov/view/cdc/29957/cdc_29957_DS1.pdf

CRISPR-Cas systems for editing, regulating and targeting genomes

The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. The deamination of adenine yields inosine, which is treated as guanine by polymerases, but no enzymes are known to deaminate adenine in DNA. Here we describe adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA. We evolved a transfer RNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9 mutant. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs that convert targeted A•T base pairs efficiently to G•C (approximately 50% efficiency in human cells) with high product purity (typically at least 99.9%) and low rates of indels (typically no more than 0.1%). ABEs introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells. Together with previous base editors, ABEs enable the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.

/pdf/programmable-base-editing-of-a-t-to-g-c-in-genomic-dna-rn1bxgz6yb.pdf

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

A recently developed adenine base editor (ABE) efficiently converts A to G and is potentially useful for clinical applications. However, its precision and efficiency in vivo remains to be addressed. Here we achieve A-to-G conversion in vivo at frequencies up to 100% by microinjection of ABE mRNA together with sgRNAs. We then generate mouse models harboring clinically relevant mutations at Ar and Hoxd13, which recapitulates respective clinical defects. Furthermore, we achieve both C-to-T and A-to-G base editing by using a combination of ABE and SaBE3, thus creating mouse model harboring multiple mutations. We also demonstrate the specificity of ABE by deep sequencing and whole-genome sequencing (WGS). Taken together, ABE is highly efficient and precise in vivo, making it feasible to model and potentially cure relevant genetic diseases. CRISPR-based base editors allow for single nucleotide genome editing in a range of organisms. Here the authors demonstrate the in vivo generation of mouse models carrying clinically relevant mutations using C→T and A→G editors.

/pdf/efficient-generation-of-mouse-models-of-human-diseases-via-p9gafrxed2.pdf

Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing

Visible infrared imaging radiometer suite (VIIRS) day/night band (DNB) data has been used to detect lit boats during night as it is very sensitive to low radiances. The existing methods for boat detection from VIIRS DNB data are mainly based on thresholds that are estimated by the statistical characteristics of pixels or artificial experience. This may generate detection errors and poor adaptability due to the lack of characterization of boat lights. In this paper, a two-step threshold detection algorithm based on the point spread and the radiative characteristics of nightlight point sources is proposed, so that the interference from adjacent pixels could be reduced as much as possible and a reasonable threshold could be determined. Meanwhile, this algorithm is applied to three study areas, namely the sea area around Tianjin Port in Bohai Sea, the sea area around Shanghai Port in East China Sea, and the sea area around Port Sulphur in Gulf of Mexico. It is demonstrated that the detection precision of the proposed algorithm reaches up to 90% and the recall rate reaches up to 85% in three areas when validated by visual interpretation, and the precision is 85.71% when validated by automatic identification system (AIS) data in the study area of the sea area around Port Sulphur in Gulf of Mexico, which approximately increases by 5% compared with the previous algorithm.

Automatic boat detection based on diffusion and radiation characterization of boat lights during night for VIIRS DNB imaging data.

The invention relates to the field of plant gene engineering. Particularly, the invention relates to a method for creating new herbicide-resistant plants by a plant base editing technology and screening endogenous gene mutation sites capable of enabling the plants to have herbicide resistance. The invention also relates to application of the identified mutated endogenous resistance genes in crop breeding.

Generation and application of herbicide-resistant gene

The present invention discloses a method for site-directed modification of whole plant through gene transient expression. The method as provided for conducting site-directed modification to a target fragment of a target gene in a whole plant comprises the following steps: transiently expressing a sequence-specific nuclease in said plant, wherein a whole plant is used as the subject for transient expression, said sequence-specific nuclease targets and cleaves said target fragment, thereby the site-directed modification is achieved via the self DNA repairing of said plant. In the present invention, tissue culture is omitted by transient expression of the sequence-specific nuclease; mutation is obtained at whole plant level; the method is independent of the genotype and recipient, and thus can be applied to various varieties of various species; T1 mutants can be obtained directly and the mutation can be stable inherited; more importantly, the mutant plant as obtained is free of exogenous genes, and thus have higher bio-safety.

Method for conducting site-specific modification on entire plant via gene transient expression

Genome engineering technologies enable the precise modification, regulation and tagging of genomic loci in living cells and organisms, leading to a broad range of applications from basic biology to biotechnology and biomedicine. For many years, precise genome manipulation has heavily relied on the homologous recombination (HR)-based gene targeting strategy, which has been limited to several organisms (yeast, mouse and human). However, recent revolutionary findings on bacterial RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systemshave led to a rangeof simple, fast and efficient genome engineering technologies, which are applicable to a wide range of organisms, including species that are recalcitrant to genetic manipulation via the traditional HR-based method. With its rapid development over the past few years, CRISPR-Cas9 and its variants have become the most powerful and versatile platforms for genetic and epigenetic editing, and can efficiently fulfill targeted genome editing, gene expression regulation, genome imaging, epigenetic modifications, base mutations and functional genomic screening. Obviously, CRISPR-Cas9 technologies, after overcoming the difficulties in genomic modifications that used to cause a bottleneck in the post-genomic era, will pave the way for the progress of functional genomics and promote its broad application in biotechnology and biomedicine, such as in the generation of disease models to reveal pathological mechanisms and enable drug discovery, the enhancement of crop and livestock production to obtain high-quality agricultural products, the construction of transgenic bioreactors to obtain bioproducts at low cost such as biofuels and the development of genetic therapies to cure human diseases. Since the advent of CRISPR-Cas9 in 2013, genome editing has become one of the most rapidly growing areas in science and has drawn much attention in recent years. Chinese scientists have played a significant role in promoting thedevelopment of the field by making enormous achievements over the last 5 years, such as the first generation of targeted gene-modified model organisms, which had previously been extremely difficult to achieve, including rat, zebrafish and monkey, and the development of human disease models using large animals such as non-human primates and pigs, the correction of genetic defects in mice, the establishment of CRIPSR-Cas9-mediated highthroughput screening systems for functional genomics, successful genome editing in insects, efficient genome modification of cropplants, revealing the structuresofCRISPR-Cas systemsand so on. To reflect the state-of-the-art nature of genome editing research in China, this special topic of National Science Review presents three timely review articles and three insightful perspectives, along with three interesting research highlights and a valuable interview. The review article by Yanfei Mao and colleagues discusses the progress and challenges in genome editing in plants, which has a long history with remarkable recent progress. The review article by Jianguo Zhao and co-authors describes an overview of the current state and future prospects of genome editing in large animals, which is critical for human disease modeling, regenerative medicine and the improvement of agricultural livestocks. The review article by Yuwei Zhu and Zhiwei Huang focuses on the recent advances in structural studies of CRISPR-Cas, which is regarded as an important basis for the efficient application of CRISPR-Cas as a genome editing tool. In their perspective article, Jun Xu et al. discuss the current state of research and challenges regarding genome editing in insects, which has been greatly enhanced by the development of CRISPR-Cas9 technologies. The perspective article by Zhuo Zhou and Wensheng Wei focuses on high-throughput CRISPR-Cas9-mediated genetic screening for non-coding genomes, which is a powerful approach for interrogating the biological and physiological functions of non-coding genetic elements. The perspective article by Jiang Jing and co-authors proposes a huge project, referred to as genome tagging project, based on ‘artificial spermatids’ and CRISPR-Cas9 technologies, in which all protein coding genes will be endogenously tagged in mice using a standard tag. Three research highlights introduce recent key advances achieved by Chinese scientists in genome editing research. The research highlight by Feng Zhang andDaniel F. Voytas reports a recent significant advance in genome editing in plants, in which gene expression has been successfully regulated at the translational level through the editing of upstream open reading frames. Chengzu Long highlights recent achievements in precise and predictable CRISPR-Cas9-mediated DNA fragment editing, which may lead to a higher chance of obtaining desired editing outcomes. The highlight article by Yuyu Niu discusses the SIRT6 mutant monkey generated by zygote injection of CRISPR-Cas9, representing a key advance in genome editing in large animals. Finally, an interview with David Liu, who is the inventor of the CRISPR-Cas-mediated base editor technology, is also included in this special topic to share his personal views on CRISPR-Cas technology and prospects for the field of genome editing science.

/pdf/preface-to-the-special-topic-on-genome-editing-research-in-4cfyxsaos0.pdf

Preface to the special topic on genome editing research in China

/pdf/discovery-of-deaminase-functions-by-structure-based-protein-1m3fre13.pdf

Caixia Gao

Papers

Automatic boat detection based on diffusion and radiation characterization of boat lights during night for VIIRS DNB imaging data.

Generation and application of herbicide-resistant gene

Method for conducting site-specific modification on entire plant via gene transient expression

Preface to the special topic on genome editing research in China

Discovery of deaminase functions by structure-based protein clustering