Entries by zu

Global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using PacBio sequencing Nextomics program

2018-05-18 /0 Comments/in /by

In April 2018, Nextomics joins hands with research group of Xiaofeng Gu, biotechnology research institute, Chinese academy of agricultural sciences, and research group of Hao Yu, department of biological sciences and Temasek life sciences laboratory, National University of Singapore, to publish a paper titled as “DNA N6-Adenine Methylation in Arabidopsis thaliana” in the journal of Development Cell. […]

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

2018-05-09 /0 Comments/in /by

Nature                 Published: 09 May 2018 Abstract:Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat1,2. Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule […]

Long-read sequencing technology generate a heated discussion in The Jackson Laboratory

2018-05-04 /0 Comments/in /by

As a large number of highly impact articles which based on the long-read sequencing technology were published, the world’s top medical genomics Laboratory The Jackson Laboratory for Genomic Medicine held a long-read sequencing workshop on April 23 to 25, 2018. Hundreds of experts and scholars in the field of biology, bioinformatics, medical genetics from across […]

Piercing the dark matter: bioinformatics of long- range sequencing and mapping

2018-03-29 /0 Comments/in /by

Nature Reviews                 29 March 2018 Abstract：Several new genomics technologies have become available that offer long- read sequencing or long- range mapping with higher throughput and higher resolution analysis than ever before. These long- range technologies are rapidly advancing the field with improved reference genomes, more comprehensive variant identification and more complete views of transcriptomes and epigenomes. However, they also require […]

Linear assembly of a human centromere on the Y chromosome

2018-03-19 /0 Comments/in /by

Nature Biotechnology     Published: 19 March 2018 Abstract：The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of nearidentical tandem repeats in centromeres. We implemented a nanopore sequencing strategy to generate high-quality reads that span hundreds of kilobases of highly repetitive DNA in a human Y chromosome centromere. Combining these data with short-read variant validation, we assembled and characterized the […]

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

2018-02-07 /0 Comments/in /by

Nature Communications      Published: 07 February 2018 Abstract：The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb […]

Nanopore sequencing and assembly of a human genome with ultra-long reads

2018-01-29 /0 Comments/in /by

Nature Biotechnology    Published: 29 January 2018 Abstract:We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone […]

The axolotl genome and the evolution of key tissue formation regulators

2018-01-24 /0 Comments/in /by

Nature          Published: 24 January 2018 Abstract:Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new […]