A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system
A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system
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DOI：
10.1093/gigascience/giz122
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发表时间：
2019-10-01
期刊：
影响因子：
9.2
通讯作者：
Geib, Scott M.
中科院分区：
文献类型：
--
作者：
Kingan, Sarah B.;Urban, Julie;Geib, Scott M.
背景：高质量的参考基因组是节肢动物应用和基础研究的重要工具。长读长测序技术可用于生成比替代技术更完整和连续的基因组组装体；然而，与下一代测序相比，长读长方法历来具有更高的输入 DNA 要求和更高的成本，这成为其在许多样本上使用的障碍。在这里，我们使用单个 Pacific Biosciences SMRT 细胞展示了现场收集的成年雌性斑点灯笼蝇（Lycorma delicatula）的 2.3 Gb 从头基因组组装。斑点灯笼蝇是最近在美国东北部发现的一种入侵物种，可能会损害该地区重要经济作物。结果：来自 1 个个体的 DNA 用于制作 1 个标准的、大小选择的文库，平均 DNA 片段大小约为 20 kb。该文库在 1 个 Sequel II SMRT Cell 8M 上运行，生成总共 132 Gb 的长读序列，其中 82 Gb 来自独特的文库分子，相当于基因组的 36 倍覆盖率。通过保守基因集分析估计，该组装具有高连续性（重叠群 N50 长度 = 1.5 Mb）、完整性和序列水平准确性（96.8% 的保守基因完整且没有移码错误）。此外，可以将一半以上的二倍体基因组分离成两个独立的单倍型。该组装还恢复了 2 个已知与 L. delicatula 相关的微生物共生体基因组，每个微生物基因组被组装成单个重叠群。结论：我们证明，野外采集的节肢动物可用于快速生成高质量的基因组组装，这对于新兴入侵物种、疾病媒介或濒危物种保护工作的项目来说是一种有吸引力的方法。
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 similar to 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 similar to 36x 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.