Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished g
Shotgun DNA sequencing has been used to build contiguous sequence information of entire chromosomes1. However, previous sequencing reads were too short to resolve the order of repetitive sequences, because the repeats were longer than an individual read, or sequence variations between two tandem copie...
Zhang,J. et al. (2016b) Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci. Data, 10.1038/sdata.2016.76.Zhang,J. et al. (2016b) Building two reference-quality indica rice genomes with clone-based PacBio long-read and Illumina ...
Despite the potential importance of TE-G transcripts in plant developmental traits and environmental responses, limitations of short-read RNA sequencing and a lack of bioinformatic pipelines have hindered the detection and comprehensive analyses of these transcripts in plants. The recent development of lo...
Sampling, sequencing, read mapping, and variant calling All samples analyzed in this study were collected and identified by the authors. We collected 26 populations spanning all known distributional regions ofQ. longinuxin Taiwan (Fig.S1a; TableS1). Three populations in Southern Taiwan (SK, LZ,...
substantial number of co-occurring strains remained in draft status [21]. The proof of concept that it is possible to de novo assemble finished metagenome-assembled genomes (MAG) of all dominant taxons in a natural microbial community based on long-read single molecule sequencing data is thus ...
Transcriptome sequencing indicates that H36L18.2 produces a mature polyadenylated RNA of ∼600 nt after the removal of two introns and trans-splicing to the SL1 splice leader (Gerstein et al., 2010) (Figure 2A). We found that ny10 was a large, ∼80 kb deletion encompassing 32 ...
The genomes of eukaryotes typically comprise a high percentage of duplicated genes. It has been proposed that gene duplication is the major mechanism for the origin of new gene function and that the refashioning of duplicate genes is a major contributor to the origin of adaptive evolutionary novelti...
The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were ...
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 1