Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
December 2017
Authors:
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, et al.
Info:
Scientists at Erasmus Medical Center determined that analysis of genome-wide methylation is challenging when fragment sizes are too small and that better epigenetic results are possible with MeD-seq. The enzyme LpnPI, they found, “is blocked by a fragment size smaller than 32 bp.” The team used PippinHT to purify PCR products prior to sequencing on the Illumina HiSeq 2500.
Citation:
Genome Research
https://genome.cshlp.org/content/28/1/88
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
November 2017
Authors:
Mircea Cretu Stancu, Markus van Roosmalen, Ivo Renkens, Marleen Nieboer, et al.
Info:
Scientists used the Oxford MinION nanopore sequencer with a novel pipeline, NanoSV, to detect structural variants from the genomes of two patients. They found that long reads are better than short reads at detecting events such as de novo chromothripsis rearrangements. The team used PippinHT for size-selecting libraries prior to sequencing.
Citation:
Nature Communications 8: 1326 (2017)
doi: 10.1038/s41467-017-01343-4
Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
November 2017
Authors:
Bing Cheng, Agnelo Furtado, Robert Henry
Info:
In this study, researchers generated the transcriptome of the tetraploid Arabica coffee bean, focusing on caffeine and sucrose genes for in-depth analysis. They used the PacBio Iso-Seq method with BluePippin selection for four library size ranges.
Citation:
GigaScience, Volume 6, Issue 11, Pages 1–13
doi: 10.1093/gigascience/gix086
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
October 2017
Authors:
Maximilian Schmidt, Alxander Vogel, Alisandra Denton, Benjamin Istace, et al.
Info:
Scientists used Oxford Nanopore technology to sequence Solanum pennellii, a wild species of tomato. They generated a median read length of nearly 12 Kb and produced an assembly with a contig N50 of 2.5 Mb. The high error rate was reduced by polishing with Illumina reads. The team enriched for long reads by using BluePippin to remove smaller fragments prior to sequencing.
Citation:
The Plant Cell
doi: 10.1105/tpc.17.00521
A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
October 2017
Authors:
Changsong Zou, Aojun Chen, Lihong Xiao, Heike Muller, et al.
Info:
Scientists deployed several sequencing platforms to characterize the genome of Chenopodium quinoa, an important and highly nutritious cereal crop. They analyzed the assembly to better understand the plant’s remarkable stress tolerance and its genomic evolution. SageELF was used to prepare DNA fractions for PCR-free library construction in an Illumina workflow.
Citation:
Cell Research (2017) 27, 1327–1340 (2017)
doi:10.1038/cr.2017.124