Aim Recent changes in land use have led to substantial loss and fragmentation of semi-natural grasslands. We assessed the relative effect current historical landscape composition, change on genetic diversity gene flow a characteristic grassland plant. Location Calcareous grasslands Muhu Saaremaa islands Western Estonia, Europe. Methods used methods study patterns plant Primula veris. applied hi...

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3,637,446 entries/2,272,231,889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing r...

UNLABELLED Recent advances in high-throughput sequencing technologies have enabled us to sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cell contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and an accurate so...

The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platfo...

The advent of high-throughput sequencing techniques, together withbisulfite treatment of the DNA, allows for genome methylation profiling at asingle cytosine resolution. Some modern tools, as MethylExtract [1], are alsoable to detect variation (SNVs) using the same bisulfite sequencing library,which is crucial for many downstream analyses, for example when decipheringthe imp...

The next-generation sequencing technologies are able to produce millions of short sequence reads in a high-throughput, cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also started to change the landscape of life sciences. Here, I survey their major applications ranging from whole-genome sequencing and resequencing, single nucleotide pol...

Although there has been a long history of cultivation and research on Nymphaea, the taxonomic relationships evolutionary among Nymphaea species remain controversial. The chloroplast (cp) genome can provide new method to determine origin, evolution, phylogenetic Nymphaea. complete cp genomes seven were sequenced by high-throughput sequencing technology, structural characteristics analyzed. had r...

Because of the time and cost associated with Sanger sequencing of complete human mtDNA genomes, practically all evolutionary studies have screened samples first to define haplogroups and then either selected a few samples from each haplogroup, or many samples from a particular haplogroup of interest, for complete mtDNA genome sequencing. Such biased sampling precludes many analyses of interest....

Base-calling accuracy is crucial for high-throughput DNA sequencing and downstream analysis such as read mapping and genome assembly. Accordingly, we made an endeavor to reduce DNA sequencing errors of Illumina systems by correcting three kinds of crosstalk in the cluster intensity data. We discovered that signal crosstalk between adjacent clusters accounts for a large portion of sequencing err...

Rapid progress in high-throughput sequencing (HTS) has enabled the molecular characterization of mutational landscapes in heterogeneous populations and has improved our understanding of clonal evolution processes. Analyzing the sensitivity of detecting genomic mutations in HTS requires comprehensive profiling of sequencing artifacts. To this end, we introduce MERIT, designed for in-depth quanti...