Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
November 2016
Authors:
Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, et al.
Info:
A large team of scientists in Asia, Europe, and the U.S. collaborated for this study of Tetrahymena thermophile, for which they produced a complete sequence assembly. They also analyzed important genomic features such as rearrangement and evolutionary history. Pippin Prep was used for size selection prior to sequencing on the Illumina HiSeq 2000.
Citation:
eLife
DOI: 10.7554/eLife.19090.001
Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data
September 2016
Authors:
Jianwei Zhang, Ling-Ling Chen, Shuai Sun, et al.
Info:
In this paper, researchers report generating two reference-quality genome assemblies for Oryza sativa subspecies. They publicly released both assemblies, which were built using PacBio and Illumina sequencing technology. For the PacBio work, scientists used BluePippin to size-select 20 kb libraries prior to sequencing.
Citation:
Scientific Data 3, Article number: 160076 (2016)
doi:10.1038/sdata.2016.76
Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolaceaS4054 Lacking the Malic Enzyme
September 2016
Authors:
Mariane S. Thøgersen, Marina W. Delpin, Jette Melchiorsen, Mogens Kilstrup, Maria Månsson, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Kristian F. Nielsen, and Lone Gram
Info:
A team of scientists analyzed biological compounds produced by Pseudoalteromonas luteoviolacea, a marine bacterium. They determined that the compounds, suspected to have antibacterial activity, were not effective in that role and that the bacterium may be producing other undiscovered compounds that achieve this function. Sequencing was conducted with PacBio after size-selection with BluePippin for 10 kb libraries.
Citation:
Front Microbiol. 2016; 7: 1461.
doi: 10.3389/fmicb.2016.01461
The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads
August 2016
Authors:
Jeremy R. Shearman, Chutima Sonthirod, Chaiwat Naktang, Wirulda Pootakham, Thippawan Yoocha, Duangjai Sangsrakru, Nukoon Jomchai, Somvong Tragoonrung, and Sithichoke Tangphatsornruang
Info:
Scientists in Thailand used long-read sequencing to assemble the mitochondrial genome of a sugarcane cultivar from southeast Asia, producing two circular chromosomes. The project supports theories that all modern commercial hybrid plants descend from S. officinarum plants in New Guinea. BluePippin size selection was used to produce 20 kb libraries for PacBio sequencing.
Citation:
Sci Rep. 2016; 6: 31533.
doi: 10.1038/srep31533
A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘mozuku’ biology
August 2016
Authors:
Koki Nishitsuji, Asuka Arimoto, Kenji Iwai, Yusuke Sudo, Kanako Hisata, Manabu Fujie, Nana Arakaki, Tetsuo Kushiro, Teruko Konishi, Chuya Shinzato, Noriyuki Satoh and Eiichi Shoguchi
Info:
Scientists from Japan sequenced the genome of Cladosiphon okamuranus, an edible seaweed popular in markets in Okinawa. Their analysis found more than 13,000 protein-coding genes in the 140 Mb genome. Libraries were purified with BluePippin before sequencing on Illumina MiSeq and HiSeq instruments
Citation:
Nature Methods (2016)
doi: 10.1093/dnares/dsw039