Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.
Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA.
G3 (Bethesda). 2021 Sep 27;11(10). doi: 10.1093/g3journal/jkab255.
Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce's disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.
玻璃翅实蝇（半翅目：叶蝉科），俗称玻璃翼蝉，是一种木质部取食叶蝉，也是 Xylella fastidiosa 的重要农业害虫传播媒介，该细菌可引起葡萄的皮尔氏病和多种其他焦枯病。目前来自贝勒医学院 i5k 试点项目的玻璃翅实蝇参考基因组是一个 14 亿碱基对的组装体，包含 110000 个支架，但仍有很大的缺口，这使得鉴定基因变得困难。为了改进这一工作，我们使用了牛津纳米孔长读测序技术与 Illumina 测序reads 的组合，生成了一个更好的加利福尼亚州（图莱里县）野生捕获的玻璃翅实蝇个体的全基因组序列的组装和首次注释。改进后的玻璃翅实蝇参考基因组组装长度为 19.3 亿碱基对（21254 个支架，N50=650 兆碱基，BUSCO 完整性=94.3%），其中 33.06%的基因组被屏蔽为重复序列。总共预测了 108762 个基因模型，包括 98296 个蛋白质编码基因和 10466 个 tRNA 基因。作为额外的社区资源，我们确定了 27 个感兴趣的直系同源候选基因，用于未来的实验工作，包括白色等表型标记基因。此外，作为组装过程的一部分，我们生成了四个共生体宏基因组组装基因组，包括一个高质量的近完整 170 兆碱基对的沃尔巴克氏体基因组（1 个支架，CheckM 完整性=99.4%）。玻璃翅实蝇的改进基因组组装和注释、精选的候选基因集以及共生体 MAG 将成为玻璃翅实蝇未来研究的宝贵资源。
