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 female specimen collected in Reading, Berks County, Pennsylvania 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.
Supporting files for the manuscript "A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System", include several intermediate versions of the assembly (raw output from Falcon, raw output from Falcon unzip, etc.) as well as the final assembly primary contigs and haplotigs (for the regions of the genome that were phased).
- Final Assembly file zip
Primary and haplotigs contigs in fasta format. File slf.8M.final.primary....
- Falcon Raw assembly, polished with arrowzip
Raw Primary contig assembly prior to falcon unzip. Contigs were polished...
- Fasta file of contig assemblies of the two symbiont genomeszip
Contains contig fasta files for Sulcia (Sulcia_muelleri.fa) and Vidania (...
- Haplotig placement file in PAF formatData
Final assembly placement file , describing the placement of haplotigs on the...
- Falcon Unzip assembly Polished with arrow Data
Falcon unzip assembly both the primary and haplotigs, unfiltered
|Release Date|| |
|Spatial / Geographical Coverage Area|| |
POLYGON ((-75.915994048119 40.335385813355, -75.915994048119 40.346376494447, -75.897797942162 40.346376494447, -75.897797942162 40.335385813355))
|Spatial / Geographical Coverage Location|| |
Female specimen sequenced collected in Reading, Berks County, Pennsylvania (40.34 N, 75.91 W)
Ag Data Commons
|Temporal Coverage|| |
August 26, 2018
|Contact Name|| |
Geib, Scott M.
|Public Access Level|| |
|Program Code|| |
005:040 - Department of Agriculture - National Research
|Bureau Code|| |
005:18 - Agricultural Research Service