Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.

Here, we describe single-tube long fragment read (stLFR), a technology that enables sequencing of data from long DNA molecules using economical second-generation sequencing technology. It is based on adding the same barcode sequence to subfragments of the original long DNA molecule (DNA cobarcoding). To achieve this efficiently, stLFR uses the surface of microbeads to create millions of miniaturized barcoding reactions in a single tube. Using a combinatorial process, up to 3.6 billion unique barcode sequences were generated on beads, enabling practically nonredundant cobarcoding with 50 million barcodes per sample. Using stLFR, we demonstrate efficient unique cobarcoding of more than 8 million 20- to 300-kb genomic DNA fragments. Analysis of the human genome NA12878 with stLFR demonstrated high-quality variant calling and phase block lengths up to N50 34 Mb. We also demonstrate detection of complex structural variants and complete diploid de novo assembly of NA12878. These analyses were all performed using single stLFR libraries, and their construction did not significantly add to the time or cost of whole-genome sequencing (WGS) library preparation. stLFR represents an easily automatable solution that enables high-quality sequencing, phasing, SV detection, scaffolding, cost-effective diploid de novo genome assembly, and other long DNA sequencing applications.

Cockroaches use diverse strategies to self-right on the ground.

Terrestrial animals often must self-right from an upside-down orientation on the ground to survive. Here, we compared self-righting strategies of the Madagascar hissing, American and discoid cockroaches on a challenging flat, rigid, low-friction surface to quantify the mechanical principles. All three species almost always self-righted (97% probability) when given time (30 s), frequently self-righted (63%) on the first attempt, and on that attempt did so in 1 s or less. When successful, two of the three species gained and used pitch and/or roll rotational kinetic energy to overcome potential energy barriers (American 63% of all attempts and discoid 78%). By contrast, the largest, heaviest, wingless cockroach (Madagascar hissing) relied far less on the energy of motion and was the slowest to self-right. Two of the three species used rolling strategies to overcome low potential energy barriers. Successful righting attempts had greater rolling rotation than failed attempts as the center of mass rose to the highest position. Madagascar hissing cockroaches rolled using body deformation (98% of all trials) and the American cockroach rolled using leg forces (93%). By contrast, the discoid cockroach overcame higher and a wider range of potential energy barriers with simultaneous pitching and rolling using the wings (46% of all trials) and legs (49%) equally to self-right. Our quantification revealed the performance advantages of using rotational kinetic energy to overcome the potential energy barrier and rolling more to lower it, while maintaining diverse strategies for ground-based self-righting.

Terradynamically streamlined shapes in animals and robots enhance traversability through densely cluttered terrain.

Many animals, modern aircraft, and underwater vehicles use fusiform, streamlined body shapes that reduce fluid dynamic drag to achieve fast and effective locomotion in air and water. Similarly, numerous small terrestrial animals move through cluttered terrain where three-dimensional, multi-component obstacles like grass, shrubs, vines, and leaf litter also resist motion, but it is unknown whether their body shape plays a major role in traversal. Few ground vehicles or terrestrial robots have used body shape to more effectively traverse environments such as cluttered terrain. Here, we challenged forest-floor-dwelling discoid cockroaches (Blaberus discoidalis) possessing a thin, rounded body to traverse tall, narrowly spaced, vertical, grass-like compliant beams. Animals displayed high traversal performance (79 ± 12% probability and 3.4 ± 0.7 s time). Although we observed diverse obstacle traversal strategies, cockroaches primarily (48 ± 9% probability) used a novel roll maneuver, a form of natural parkour, allowing them to rapidly traverse obstacle gaps narrower than half their body width (2.0 ± 0.5 s traversal time). Reduction of body roundness by addition of artificial shells nearly inhibited roll maneuvers and decreased traversal performance. Inspired by this discovery, we added a thin, rounded exoskeletal shell to a legged robot with a nearly cuboidal body, common to many existing terrestrial robots. Without adding sensory feedback or changing the open-loop control, the rounded shell enabled the robot to traverse beam obstacles with gaps narrower than shell width via body roll. Such terradynamically 'streamlined' shapes can reduce terrain resistance and enhance traversability by assisting effective body reorientation via distributed mechanical feedback. Our findings highlight the need to consider body shape to improve robot mobility in real-world terrain often filled with clutter, and to develop better locomotor-ground contact models to understand interaction with 3D, multi-component terrain.