Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
National Center for Biotechnology,, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia.
Sci Rep. 2021 May 11;11(1):9987. doi: 10.1038/s41598-021-89091-w.
The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ([Formula: see text] 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.
红棕象甲 Rhynchophorus ferrugineus（鞘翅目：象甲科）是一种具有重要经济意义的入侵物种，它攻击世界各地的多种棕榈树。更好地了解 R. ferrugineus 的基因内容和功能有可能为害虫防治策略提供信息，从而减轻该物种造成的经济和生物多样性损失。我们使用 10x Genomics 连接读取测序，从一个具有适度测序覆盖度的杂合个体（[Formula: see text] 62x）中生成了 R. ferrugineus 的单倍型解析二倍体基因组组装。与保守的单拷贝节肢动物直系同源物进行基准测试表明，我们的 R. ferrugineus 基因组组装中的两个假单倍型在基因内容方面都非常完整，并且不会受到该物种最近发布的混合组装中存在的单倍型诱导重复 artefacts 的影响。我们组装中大的假单倍型的注释为 R. ferrugineus 提供了 23,413 个编码蛋白的基因座的证据，包括超过 13,000 个用 GO 术语注释的预测蛋白和超过 6,000 个由高质量 Iso-Seq 转录组数据独立支持的基因座。我们的组装还包括了之前使用 RNA-seq 转录组数据识别的 95%的 R. ferrugineus 化学感觉、解毒和神经肽相关转录本，并为这些和其他功能相关基因的分子分析提供了一个平台，这有助于指导这种广泛分布的昆虫害虫的管理。
