A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

Abstract

Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

Investigational Assay for Haplotype Phasing of the Huntingtin Gene

“…Superior performance is now achievable with the PacBio Sequel II platform, which is reported to provide maximum subread lengths of >200 kb, an insert (subread) length N50 of 22.3 kb, and a polymerase read length N50 of 41.7 kb, yielding 131.6 Gb of total sequence. 41 …”

Biodiversity genomics of small metazoans: high qualityde novogenomes from single specimens of field-collected and ethanol-preserved springtails

“…Both species were fieldcollected and preserved in ethanol. The final assemblies were of high contiguity and completeness, on par with recent genomes sequenced on PacBio from single insects (Kingan et al, 2019b(Kingan et al, , 2019c, and also on par with the best reference genome for a Collembola so far, Sinella curviseta, which was DNA sequenced from 500 specimens maintained in culture (Zhang et al, 2019).…”

“…For example, PacBio recently released a "Low input library preparation" protocol, with a recommended requirement of 150 ng DNA (https://www.pacb.com/wp-content/uploads/Procedure-Checklist-Preparing-HiFi-Libraries-from-Low-DNA-Input-Using-SMRTbell-Express-Template-Prep-Kit-2.0.pdf), down to 50 ng DNA (Kingan et al 2019a). This allows amplification free genome-sequencing of small metazoans in the size range of single mosquitoes (Kingan et al, 2019b(Kingan et al, , 2019c. But as most metazoans are smaller than a single mosquito, this 50--150 ng DNA requirement will generally prove to be already too high.…”

Perspective: shedding light on spotted lanternfly impacts in the USA

“…Along these lines, the SLF genome and endosymbiont genomes have recently been sequenced. 19 However, innovative emerging technologies in place to control other pests (for which there are much more extensive '-omics" resources) should be examined for potential applicability to SLF.…”