SilkDB: a knowledgebase for silkworm biology and genomics

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn

The diploid genome sequence of an Asian individual

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Achieving a Collapsible, Strong, and Highly Thermally Conductive Film Based on Oriented Functionalized Boron Nitride Nanosheets and Cellulose Nanofiber

Boron nitride nanosheet (BNNS) films receive wide attention in both academia and industry because of their high thermal conductivity (TC) and good electrical insulation capability. However, the brittleness and low strength of the BNNS film largely limit its application. Herein, functionalized BNNSs (f-BNNSs) with a well-maintained in-plane crystalline structure were first prepared utilizing urea in the aqueous solution via ball-milling for the purpose of improving their stability in water and enhancing the interaction with the polymer matrix. Then, a biodegradable and highly thermally conductive film with an orderly oriented structure based on cellulose nanofibers (CNFs) and f-BNNSs was prepared just by simple vacuum-assisted filtration. The modification of the BNNS and the introduction of the CNF result in a better orientation of the f-BNNS, sufficient connection between f-BNNS themselves, and strong interaction between f-BNNS and CNF, which not only make the prepared composite film strong and tough but also possess higher in-plane TC. An increase of 70% in-plane TC, 63.2% tensile strength, and 77.8% elongation could be achieved for CNF/f-BNNS films, compared with that for CNF/BNNS films at the filler content of 70%. Although at such a high f-BNNS content, this composite film can be bended and folded. It is even more interesting to find that the in-plane TC could be greatly enhanced with the decrease of the thickness of the film, and a value of 30.25 W/m K can be achieved at the thickness of ∼30 μm for the film containing 70 wt % f-BNNS. We believe that this highly thermally conductive film with good strength and toughness could have potential applications in next-generation highly powerful and collapsible electronic devices

Completely Green Approach for the Preparation of Strong and Highly Conductive Graphene Composite Film by Using Nanocellulose as Dispersing Agent and Mechanical Compression

Graphene films receive tremendous attention due to their ultrahigh electrical and thermal conductivities, which show great application prospects in modern electronic devices. However, the brittleness and low strength of graphene films largely limit their use in advanced applications. And the preparation processes of graphene films reported so far are also not completely green. In this work, a novel strong and green graphene composite film with outstanding electromagnetic interference shielding effectiveness (EMI SE), electrical and thermal conductivities was successfully fabricated by using nanofibrillated cellulose (NFC) as dispersing agent and mechanical compression. In this way, graphene nanosheets (GNs) were not only efficiently dispersed in the aqueous solution but also linked together by NFC to enhance mechanical strength of the prepared films. Simultaneously, mechanical compression could powerfully induce strong alignment and increase the contact area of the GNs. As a result, the optimum electrical and thermal conductivities of the obtained films reached up to 988.2 S cm^–1 and 240.5 W m^–1 K^–1, respectively, along with a high tensile strength of 61 MPa and a superior EMI SE of 43 dB with only ≈13 μm in thickness. Even more, the resultant films revealed excellent flame resistance. And the NFC can be removed by burning the films, resulting in complete graphene films with much higher electrical and thermal conductivities. The manufacturing route in our study is facile, cost-effective and completely green for the preparation of strong and highly conductive graphene-based thin films

Design and Preparation of a Unique Segregated Double Network with Excellent Thermal Conductive Property

It is still a challenge to fabricate polymer-based composites with excellent thermal conductive property because of the well-known difficulties such as insufficient conductive pathways and inefficient filler–filler contact. To address this issue, a synergistic segregated double network by using two fillers with different dimensions has been designed and prepared by taking graphene nanoplates (GNPs) and multiwalled carbon nanotubes (MWCNT) in polystyrene for example. In this structure, GNPs form the segregated network to largely increase the filler–filler contact areas while MWCNT are embedded within the network to improve the network-density. The segregated network and the randomly dispersed hybrid network by using GNPs and MWCNT together were also prepared for comparison. It was found that the thermal conductivity of segregated double network can achieve almost 1.8-fold as high as that of the randomly dispersed hybrid network, and 2.2-fold as that of the segregated network. Meanwhile, much higher synergistic efficiency (<i>f</i>) of 2 can be obtained, even greater than that of other synergistic systems reported previously. The excellent thermal conductive property and higher <i>f</i> are ascribed to the unique effect of segregated double network: (1) extensive GNPs–GNPs contact areas via overlapped interconnections within segregated GNPs network; (2) efficient synergistic effect between MWCNT network and GNPs network based on bridge effect as well as increasing the network-density

De novo assembly of a haplotype-resolved human genome.

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine