The sequencing and annotation of the Drosophila melanogaster genome, first published in 2000 through collaboration between Celera Genomics and the Drosophila Genome Projects, has provided a number of important contributions to genome research. By demonstrating the utility of methods such as whole-genome shotgun sequencing and genome annotation by a community "jamboree," the Drosophila genome es...

MicroRNAs (miRNAs) play important roles in growth, development, and response to environmental changes in plants. Based on the whole-genome shotgun sequencing strategy, more and more wheat miRNAs have been annotated. Now, there is a need for an effective technology to analyse endogenous miRNAs function in wheat. We report here that the modified barley stripe mosaic virus (BSMV)-induced miRNAs si...

The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific and directed by a conserved 15-bp chromosome breakage sequence (Cbs element). This article reports the construction of a library enriched for chromosome breakage junctions and the devel...

This report highlights the whole-genome shotgun draft sequence for a Streptococcus agalactiae strain representing multilocus sequence type (ST) 17, isolated from a colonized woman at 8 weeks postpartum. This sequence represents an important addition to the published genomes and will promote comparative genomic studies of S. agalactiae recovered from diverse sources.

Shotgun wounds can result in devastating functional and aesthetic consequences for patients. There is no consensus in terms of removing or retaining foreign bodies such as shotgun pellets. In this report a 54-year-old man who suffered from accidental shotgun wounds on the face approximately 26 years ago is presented. Although most of pellets were still present, there were no symptoms such as po...

33 T he prevailing method of determining the sequence of a long DNA segment is the shotgun sequencing approach, in which a random sampling of short fragment sequences is acquired and then assembled by a computer program to infer the sampled segment's sequence. In the early 1980s, such segments were typically on the order of 5,000 to 10,000 base pairs (5 to 10 kbp). By 1990, this method was sequ...

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), w...

In order to quantitatively comprehend the essence of whole genome shotgun sequencing, a Monte-Carlo simulation was carried out. It was estimated that even a vast genome such as human genome can be sequenced at a moderate redundancy ( 7) with a satisfactory accuracy (10 error rate), resulting in a high sequencing speed and much lower cost. Switching from a random process (i.e., shotgun) to a dir...

Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline...

The genome sequence of the soil bacterium Sphingobacterium sp. strain HMA12, the culture supernatant of which exhibited endo-β-N-acetylglucosaminidase (ENGase) activity, was examined for ENGase-encoding genes. Here, we report the characterization of new genes of ENGases, obtained by whole-genome shotgun sequencing, that are capable of specifically hydrolyzing fucose-containing oligosaccharides.