Assembly and analysis of the genome of Notholithocarpus densiflorus.

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.

High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities.

Sequencing of hypervariable regions as well as internal transcribed spacer regions of ribosomal RNA genes (rDNA) is broadly used to identify bacteria and fungi, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length using high throughput, cost-efficient second-generation sequencing. We developed a method to obtain nearly full-length rDNA by assembling single DNA molecules combining DNA co-barcoding with single-tube long fragment read technology and second-generation sequencing. Benchmarking was performed using mock bacterial and fungal communities as well as two forest soil samples.

A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.

In this chapter, we describe single-tube long fragment read (stLFR), a simple preparation method for whole-genome sequencing and physical haplotyping based on the DNA co-barcoding strategy. Similar to LFR, stLFR applies the concept of adding the same barcode to subfragments derived from the same long DNA molecule. However, instead of a 384-well plate, stLFR uses the surface of micron-sized magnetic beads to create millions of virtual compartments in a single reaction tube.

Large-Scale Complete Sequencing and Haplotyping of 1-10 kb DNA Molecules Using Short Massively Parallel Reads.

In this chapter, we describe a simple, low-cost method for making many copies of a single DNA molecule (1-10 kb in length) as a concatemer on a long DNA strand. This can enable applications requiring high-quality contiguous sequence and haplotype data from long single DNA molecules at large scale.