Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
June 2017
Authors:
Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Zsolt Balázs, et al.
Info:
Scientists from Hungary and California conducted isoform sequencing with PacBio to analyze the transcriptome of herpes simplex virus type 1. They discovered dozens of previously unidentified protein-coding genes and non-coding RNAs and found that transcription may facilitate crosstalk between distant genes. They used both BluePippin and SageELF to remove shorter fragments and focus libraries on the longest molecules.
Citation:
Front Microbiol. 2017; 8: 1079.
doi: 10.3389/fmicb.2017.01079
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
June 2017
Authors:
Jason Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
Info:
In this F1000 publication, scientists describe an evaluation of long-read sequencing technologies, finding that PacBio provides better data quality while Oxford Nanopore generates higher yield. They used SageELF to fractionate cDNAs into four contiguous size ranges.
Citation:
F1000Research 2017, 6:100
quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
May 2017
Authors:
Franchini P, Monné Parera D, Kautt AF, Meyer A
Info:
Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method on a population of Neotropical cichlid fish. Pippin Prep was used to size-select fragments prior to Illumina sequencing.
Citation:
Mol Ecol. 2017 May;26(10):2783-2795
doi: 10.1111/mec.14077
Comparative Analysis of Ralstonia solanacearum Methylomes
April 2017
Authors:
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, et al.
Info:
Scientists report results of analyzing epigenetic patterns in two strains of a plant pathogen. They determined that methylation regulates virulence and adaptation to different host plants. BluePippin was used to remove smaller library fragments prior to sequencing with PacBio.
Citation:
Front Plant Sci. 2017; 8: 504
doi: 10.3389/fpls.2017.00504
Tripartite species interaction: eukaryotic hosts suffer more from phage susceptible than from phage resistant bacteria
April 2017
Authors:
Carolin Wendling, Agnes Piecyk, Dominik Refardt, Cynthia Chibani, et al.
Info:
Scientists investigated the extent to which a bacterium’s susceptibility or resistance to prophages alters its own effect as a pathogen, finding that bacteria that were more likely to take in phages were also more harmful to their eukaryotic host organism. Whole genome sequencing was performed with PacBio, and BluePippin was used to prepare 10 Kb libraries.
Citation:
BMC Evolutionary Biology 2017 17:98