Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere
March 2017
Authors:
Henk J. Schouten, Henri vande Geest, Sofia Papadimitriou, Marian Bemer, Jan G. Schaart, Marinus J. M. Smulders, Gabino Sanchez Perez, Elio Schijlen
Info:
Scientists from Wageningen University and Research sequenced and analyzed several Arabidopsis thaliana plants to understand the mutagenic effects of Agrobacterium tumefaciens. As part of this project, they identified a 50 bp partial T-DNA insert and named it a T-DNA splinter. BluePippin was used to remove short fragments from the library prior to sequencing with PacBio.
Citation:
Plant Cell Reports, volume 36, Issue 3, pp 493–504
DOI: 10.1007/s00299-017-2098-z
Detecting DNA cytosine methylation using nanopore sequencing
February 2017
Authors:
Jared Simpson, Rachael Workman, PC Zuzarte, Matei David, LJ Dursi & Winston Timp
Info:
In this paper, scientists report developing algorithms to distinguish methylated from unmethylated DNA using the Oxford Nanopore MinION sequencer. They evaluated its performance by sequencing a human methylome. BluePippin was used to size-select libraries for 3,500 bp to 6,000 bp.
Citation:
Nature Methods 14, 407–410 (2017)
doi:10.1038/nmeth.4184
Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone
February 2017
Authors:
Adam D. Leaché, Jared A. Grummer, Rebecca B. Harris, and Ian K. Breckheimer
Info:
Scientists at the University of Washington analyzed samples collected over a 10-year period to better understand evolution of Sceloporus tristichus in a hybrid zone. They used BluePippin for size selection of libraries to 415 bp – 515 bp.
Citation:
Molecular Ecology
DOI: 10.1111/mec.14033
Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution
February 2017
Authors:
Gavin G. Rutledge, Ulrike Böhme, Mandy Sanders, Adam J. Reid, et al.
Info:
In this paper, scientists generated a new reference genome and a manually curated draft assembly for two Plasmodium species. This effort made it possible to resolve discrepancies in the Plasmodium phylogeny and indicates host-specific adaptations as the organism entered new species. Sequencing of P. malariae was performed on PacBio after size selection with BluePippin.
Citation:
Nature 542, 101–104
doi:10.1038/nature21038
Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird
February 2017
Authors:
Jennifer Walsh, Irby J. Lovette, Virginia Winder, Chris S. Elphick, Brian J. Olsen, Gregory Shriver, and Adrienne I. Kovach
Info:
Scientists at Cornell University and other institutions analyzed sparrow populations using reduced-representation sequencing to understand the genetic differences underlying a very broad range of phenotypes. They found that genetic data indicated three distinct clusters corresponding to habitat. The team used BluePippin to select 400 bp – 700 bp fragments for sequencing.
Citation:
Molecular Ecology
DOI: 10.1111/mec.14010