A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

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

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

“…For nanopore in particular, methods to achieve higher sequence accuracy 37 or circumvent PCR bias and reverse transcription length restrictions 30 have been developed. In line with the rigorous pace of improvements in the field of long reads, PacBio has recently improved their throughput 8× with the newest PacBio Sequel II system, which has been shown to gen-erate~19 and 83 Gb of consensus reads 39,70 . This study of six primary CLL samples with nanopore sequencing demonstrates the ability of the nanopore to identify and quantify cancer-specific transcript variants.…”

“…The raw accuracy of nanopore 1D cDNA sequencing is~85-87% [36][37][38] , although accuracy can change depending on iterations of the technology and library preparation methods 37 . In contrast, the long consensus reads produced by Pacific Biosciences are able to achieve much higher base accuracies 39 . Thus, software tools developed for PacBio sequencing were not developed for noisier data and may disregard raw reads with less than 99% accuracy 40 or discard assembled isoforms with too many errors 41 .…”

Perspective: shedding light on spotted lanternfly impacts in the USA

“…Given the wide range of habitats SLF inhabits, synthetic tools, such as RNAi targeting of specific SLF or SLF endosymbiont genes, may offer greater host specificity. Along these lines, the SLF genome and endosymbiont genomes have recently been sequenced . 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.…”

A high-quality de novo genome assembly from a single parasitoid wasp

“…Mostly, the amount of genomic DNA is very low when obtained from single small-sized insect, which makes it hard to meet the standard DNA input requirement of long-reads sequencing (Pacbio or Nanopore) or even short-reads sequencing (Illumina) [1, [3][4][5][6]. Over the past two decades, many insects with small body size (e. g., parasitoid wasps, aphids, many Drosophila)…”

“…However, most of insects are difficult to collect or cannot be well reared in the lab. Even if they can be reared in the lab, they might be difficult to inbreed [1, 3,6].…”