Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA.
BMC Biol. 2020 Oct 19;18(1):142. doi: 10.1186/s12915-020-00862-9.
The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.
We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.
Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
西部花蓟马（Frankliniella occidentalis (Pergande)）是一种具有全球入侵性的害虫，也是多种粮食作物、纤维作物和观赏作物的植物病毒载体。控制蓟马害虫和载体生物学、取食行为、生态学和抗药性的潜在遗传机制在很大程度上尚不清楚。为了解决这一差距，我们提供了西部花蓟马的基因组草图组装和官方基因集。
我们报告了缨翅目昆虫中第一个基因组序列。对基因组组装（大小=415.8 Mb，支架 N50=948.9 kb）的通用单拷贝同源物（BUSCO）基准测试评估与其他昆虫基因组相比，显示出一个相对完整和注释良好的组装。与迄今为止的其他昆虫基因组相比，该基因组的 GC 含量（50%）异常高。官方基因集（OGS v1.0）包含 16859 个基因，其中约 10%由我们的联盟手动验证和纠正。我们专注于手动注释、系统发育和表达证据分析，这些分析集中在与植物定殖昆虫的生活史和活动相关的主要主题上。重点包括以下几个方面：（1）与在农业环境中遇到的物质的环境感应（化学感觉受体）和解毒（CYP4、CYP6 和 CCE 酶）相关的基因的分歧进化枝和大量扩张；（2）丰富表达支持的完整唾液腺基因集；（3）IMD 先天免疫防御途径的明显缺失；以及（4）与通过新变态从幼虫发育到成虫的相关基因的发育和性别特异性表达分析，新变态是一种与昆虫纲中的不完全或完全变态不同的独特成熟形式。
西部花蓟马基因组的分析为这种昆虫害虫的多食性行为提供了深入的了解，这种害虫在广泛的植物上寻找、定殖和生存。这里提供的基因组资源使我们能够更全面地分析昆虫的进化和生物学，为当代基于昆虫基因组的分析提供了一个缺失的分类群。我们的研究还为其他缨翅目物种的分子和进化研究提供了基因组基准。
