We normally wait until papers come out in scientific journals before reporting on them here, but there are so many great preprints featuring Sage Science tools we couldn’t resist pointing them out. (On a side note, the rising numbers of biology-focused papers posted as preprints is a terrific trend. We’re thrilled to see the peer-review process becoming more transparent and results getting out to the community faster.)
Here are quick recaps of several preprints, all available through bioRxiv.
The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only
Erwin Datema, Raymond J.M. Hulzink, Lisanne Blommers, Jose Espejo Valle-Inclan, Nathalie Van Orsouw, Alexander H.J. Wittenberg, Martin De Vos
Posted: November 1, 2016
This paper from Keygene scientists used Oxford Nanopore sequencing technology to analyze the fungal pathogen Rhizoctonia solani, generating a highly contiguous 54 Mb assembly. The team focused on optimizing methods for handling high molecular weight DNA to produce the longest sequencing reads. They used BluePippin’s high-pass mode to remove smaller DNA fragments. According to the paper, this approach allows the lab to generate a low-cost eukaryotic fungal genome within a week.
Conrad P.D.T. Gillett, Andrew J Johnson, Iain Barr, Jiri Hulcr
Posted: September 12, 2016
In this preprint, scientists from the University of Florida and the University of East Anglia evaluated a sequencing-based approach to monitoring biodiversity in a region using dung beetles. Since these beetles regularly consume vertebrate dung, the contents of their intestines can reveal quite a bit about animals in the area. They sequenced samples from 10 species of dung beetles collected from a savanna region in southern Africa, and then compared the mitochondrial DNA results against public databases. Results matched animals expected in the area, such as zebra, cattle, goat, and wildebeest. DNA libraries were size-selected using the SageELF system followed by sequencing on an Illumina NextSeq.
Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing
Fabio Zanini, Johanna Brodin, Jan Albert, Richard Neher
Posted: September 25, 2016
Researchers at Stanford University, the Karolinska Institute, and the Max Planck Institute collaborated in this effort to establish more accurate and reliable methods for deep sequencing of viral genomes without the amplification biases and sequencing errors that often occur. In a study focused on sequencing populations of HIV-1, the team adjusted the standard sequencing workflow to reduce artifacts and errors. One of those changes involved replacing bead-based size selection with BluePippin sizing, which yielded a more uniform size distribution to meet the insert size needed by the MiSeq platform. With this approach, the scientists were able to detect rare mutations down to 0.2% and to avoid PCR recombination.
Two novel genes discovered in human mitochondrial DNA using PacBio full-length transcriptome data
Gao Shan, Xiaoxuan Tian, Yu Sun, Zhenfeng Wu, Zhi Cheng, Pengzhi Dong, Bingjun He, Jishou Ruan, Wenjun Bu
Posted: October 6, 2016
This work from scientists at Nankai University and Tianjin University of Traditional Chinese Medicine focuses on mitochondrial biology. They used the Iso-Seq method to generate “the first full-length human mitochondrial transcriptome from the MCF7 cell line based on the PacBio platform.” As part of the study, the team used transcriptome data publicly released by PacBio, for which size selection was performed on a SageELF to create six binned libraries.