Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication
March 2017
Authors:
Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, et al.
Info:
Scientists from China and the UK scanned the genomes of 352 varieties of cotton, both wild and domestic, to map variants associated with crop domestication throughout its history. They identified 19 candidate variants that may be related to fiber quality. For this project, the team used PippinHT to isolate purified DNA fragments prior to sequencing with an Illumina HiSeq 2000.
Citation:
Nature Genetics 49, 579–587 (2017)
doi:10.1038/ng.3807
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