Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses

We always keep our eyes peeled for interesting new research from scientists using Sage Science automated DNA size selection instruments, and several recent preprints caught our attention. Here’s a look:

Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome

Authors: Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, et al.

Scientists from The Jackson Laboratory for Genomic Medicine and China Medical University in Taiwan teamed up to detect structural variants in breast cancer genomes using a custom-built pipeline called Picky. They chose nanopore sequencing to generate long reads, identifying SVs with excellent sensitivity and specificity and finding that repetitive DNA was the primary source of cancer-related variation. This approach could prove useful in efforts to assess genome stability in a tumor over time. The team used BluePippin to size-select 12 Kb libraries prior to nanopore sequencing.

De novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research

Authors: Jonas Korlach, Gregory Gedman, Sarah Kingan, et al.

In this work, scientists seeking to improve upon short-read genome assemblies for two birds deployed long-read PacBio sequencing to generate new diploid assemblies. The effort yielded assemblies with megabase-sized contigs, with a 150-fold improvement in the contiguity for the zebra finch genome and 200-fold improvement for Anna’s hummingbird. Since the birds are both models for vocal learning, the higher level of completeness, correction of previous misassemblies, and more accurate gene sequences will be important for many future studies. The team used BluePippin to size libraries for zebra finch and hummingbird prior to sequencing.

CIDER-Seq: unbiased virus enrichment and single-read, full length genome sequencing

Authors: Devang Mehta, Matthias Hirsch-Hoffmann, Andrea Patrignani, et al.

Scientists developed a new method for deeply sequencing viruses that can accurately represent populations with high levels of homology across genomes. They incorporated long-read sequencing with random circular amplification enrichment and a novel de-concatenation protocol, validating their results in a large population of geminiviruses. BluePippin was used for size selection prior to the enrichment step and again during library preparation for sequencing.

Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

Authors: Derrick Thrasher, Bronwyn Butcher, Leonardo Campagna, et al.

Continuing with the avian theme, researchers used ddRAD-seq to analyze as many as 600 SNPs from up to 240 members of a population — validated in this case with a study of Malurus lamberti and other bird species. By comparing results to microsatellite markers, they determined that the ddRAD-seq method “results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients,” they report. The pipeline they present, which relies on BluePippin for DNA fragment sizing, can be used with any other bird species, and other organisms as well.

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