A high-quality genome assembly from a single, field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

Authors: KINGAN, SARAH - Pacific Biosciences Inc; URBAN, JULIE - Pennsylvania State University; LAMBERT, CHRISTINE - Pacific Biosciences Inc; BAYBAYAN, PRIMO - Pacific Biosciences Inc; Childers, Anna; Coates, Brad; Scheffler, Brian; Hackett, Kevin; KORLACK, JONAS - Pacific Biosciences Inc; Geib, Scott

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2019
Publication Date: 10/14/2019
Citation: Kingan, S.B., Urban, J., Lambert, C.C., Baybayan, P., Childers, A.K., Coates, B.S., Scheffler, B.E., Hackett, K.J., Korlack, J., Geib, S.M. 2019. A high-quality genome assembly from a single, field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System. Gigascience. 8(10):1-10. https://doi.org/10.1093/gigascience/giz122.
DOI: https://doi.org/10.1093/gigascience/giz122

Interpretive Summary: We present a high-quality reference genome for the emerging invasive pest, Lycorma delicatula (Spotted Laternfly). This pest was recently discovered in the Northeastern US and has the potential to spread broadly across the country and can impact a number of horticultural and landscape hosts. Using a new sequencing platform, the PacBio Sequel II system, as well as direct sample strategies of a wild collect host, we demonstrate the ability to rapidly and effectively reconstruct a genome for an emerging pest without the need to inbreed, rear in the laboratory, or pool many individuals into a single extraction. By leveraging the relatively high heterozygosity in a wild caught individual, a large proportion of the genome could be phased, and is represented as a true haploid assembly. Additionally, we recovered the complete genome of two important obligate symbionts of this species which have evolved to provide essential nutrition to the host, which feeds on nutrient poor plant saps. Control methods through manipulation of the host’s symbionts may be elucidated from this genomic data. 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.

Technical Abstract: 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 PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one 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 approximately 38x 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). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. 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.