BackgroundThe honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana.ResultsUsing de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes.ConclusionsThis first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-16-1) contains supplementary material, which is available to authorized users.

BackgroundNext generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery.ResultsUsing a multi-tier reduced representation library we discovered a total of 3,487 SNPs of which 2,795 contained sufficient flanking genomic sequence for SNP assay development. Using Sanger sequencing to determine the validation rate of these SNPs, we found that 86% are likely to be true SNPs. Furthermore, we designed a GoldenGate assay which contained 1,050 of the 3,487 predicted SNPs. A total of 827 of the 1,050 SNPs produced a working GoldenGate assay (79%).ConclusionsThrough combining two next generation sequencing techniques we have developed a method that allows high-throughput SNP discovery in any diploid organism without the need of a whole genome sequence or the creation of normalized cDNA libraries. The need to only perform one 454 run and one GA sequencer run allows high-throughput SNP discovery with sufficient sequence for assay development to be performed in organisms, such as common bean, which have limited genomic resources.

We report the complete genome sequence of Burkholderia gladioli BSR3, isolated from a diseased rice sheath in South Korea.Whole-genome shotgun DNA sequencing of Burkholderia gladioli BSR3, isolated from a diseased rice sheath in South Korea, was performed using the Roche/454 pyrosequencing method on a Genome Sequencer FLX system. In total, 359,799,231 and 209,679,192 bases were analyzed in single and paired-end reads, respectively. The genomic shotgun sequence data were assembled with Newbler (version 2.5.3; 454 Life Sciences). In total, 195 contigs were produced in 19 scaffolds through de novo assembly. Gaps among the contigs were closed by a combination of primer walking on gap-spanning clones and the direct sequencing of combinatorial PCR products. Coding genes and pseudogenes across the genome were predicted using Glimmer (2), GeneMarkHMM (4), and Prodigal (3) and annotated by comparison with the NCBI-NR (1). Our annotation results were verified using Artemis (5).The B. gladioli genome is 9.05 Mb and consists of two chromosomes and four plasmids. Chromosome 1 contains 4,413,616 bp (67.5% GϩC content) and 3,778 predicted coding sequences (CDS). Chromosome 2 contains 3,700,833 bp (68.6% GϩC content) and 2,926 CDS. Plasmid bgla_1p contains 276,215 bp (63.3% GϩC content and 189 CDS), plasmid bgla_2p contains 129,399 bp (62.8% GϩC content and 104 CDS), plasmid bgla_3p contains 128,650 bp (59.6% GϩC content and 94 CDS), and plasmid bgla_4p contains 403,586 bp (62.4% GϩC content and 319 CDS).Nucleotide sequence accession numbers. The sequences of the B. gladioli BSR3 chromosomes and plasmids (bgla_1g, bgla_2g, bgla_1p, bgla_2p, bgla_3p, and bgla_4p) have been deposited in GenBank

The work functions φω of MgO single crystals with its respective orientation (111), (200), and (220) have been investigated from their ion-induced secondary electron emission coefficient γ, respectively, using various ions with different ionization energies in a γ-focused ion beam system. The work function φω for MgO single crystal with (111) orientation has the lowest value, 4.22 eV, whereas it is 4.94 eV for (200) and the highest value is 5.07 eV for (220). These work functions of MgO single crystals can explain the nonzero values of the ion-induced secondary electron emission coefficient γ for Xe+ ions, whose ionization energy is 12.13 eV.

The Japanese Erwinia strain Ejp617 is a plant pathogen that causes bacterial shoot blight of pear in Japan. Here, we report the complete genome sequence of strain Ejp617 isolated from Nashi pears in Japan to provide further valuable insight among related Erwinia species.