De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)
February 2017
Authors:
Si Lok, Tara A. Paton, Zhuozhi Wang, Gaganjot Kaur, et al.
Info:
Researchers in Toronto report a high-quality draft assembly of the 2.7 Gb beaver genome using SMRT Sequencing. They include an analysis of gene content, such as enrichment for genes associated with dentition and enamel deposition. The team used BluePippin to remove fragments smaller than 15 Kb before sequencing with PacBio.
Citation:
G3: Genes, Genomes, Genetics
vol. 7 no. 2 755-773
DOI:10.1534/g3.116.038208
Complete genome sequence of Lutibacter profundi LP1Tisolated from an Arctic deep-sea hydrothermal vent system
January 2017
Authors:
Juliane Wissuwa, Sven Le Moine Bauer, Ida Helene Steen, and Runar Stokke
Info:
Scientists from the University of Bergen used PacBio sequencing to produce a complete genome assembly for Lutibacter profundi LP1T, an extremophile isolated from a biofilm on a hydrothermal vent. This is the first genome to be published for this genus. The team used BluePippin to size-select libraries for the largest fragments prior to sequencing.
Citation:
Standards in Genomic Sciences 201712:5
DOI: 10.1186/s40793-016-0219-x
Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity
January 2017
Authors:
Elizabeth Davis, Tyler Sloan, Krista Aurelius, Angela Barbour, et al.
Info:
Through a citizen science program, college students analyzed 77 soil-derived bacteria to promote genetic characterization and antibiotic discovery for the fight against drug-resistant pathogens. They chose PacBio sequencing to sequence the whole genome of one microbe. That pipeline included BluePippin to generate 20 Kb libraries.
Citation:
Microbiology Open
DOI: 10.1002/mbo3.435
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
January 2017
Authors:
Rebecca B. Dikow, Paul B. Frandsen, Mauren Turcatel, and Torsten Dikow
Info:
Researchers at the Smithsonian Institution published a high-quality draft genome, 16 transcriptomes, and a time-calibrated phylogeny for the assassin fly. They also include bioinformatics tools to help other scientists looking to produce similar resources for organisms without a reference genome. BluePippin was used to size RNA libraries prior to Illumina sequencing.
Citation:
PeerJ 5:e2951
DOI 10.7717/peerj.2951
Pharmacologic activation of estrogen receptor β increases mitochondrial function, energy expenditure, and brown adipose tissue
January 2017
Authors:
Suriyan Ponnusamy, Quynh T. Tran, Innocence Harvey, Heather S. Smallwood, et al.
Info:
Scientists in Memphis, Tenn., studied obesity in mice, finding that estrogen receptor β and its ligands had a strong anti-obesity effect, reducing weight gain and adiposity in mice without any changes to activity levels or food intake. This could indicate a new opportunity for safe anti-obesity therapeutics in humans. For this project, Pippin Prep was used for library sizing prior to sequencing on an Ion Torrent Proton.
Citation:
The FASEB Journal vol. 31 no. 1 266-281
doi:10.1096/fj.201600787RR