Wang Yan-Xia, Chen Hu-Fang, Yin Zheng-Yan, Chen Wen-Long, Lu Li-Tang
Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China; College of Tea Science, Guizhou University, Guiyang 550025, China.
College of Tea Science, Guizhou University, Guiyang 550025, China.
Genomics. 2022 Nov;114(6):110472. doi: 10.1016/j.ygeno.2022.110472. Epub 2022 Aug 31.
Toxoptera aurantii Boyer de Fonscolombe (Hemiptera: Aphididae) can attack many plant hosts, including tea (Camellia sinensis L.), citrus (Citrus spp.), lychee (Litchi chinensis Sonn.), banana (Musa spp.), and pineapple (Ananas comasus L.) among others. It is a widely distributed hexapod and one of the most destructive pests in tea plantations, causing enormous economic losses in tea production each year. A high-quality reference genome is important to study the phylogenetics and evolution of T. aurantii because its genome is highly heterozygous and repetitive. We obtained a de novo genome assembly of T. aurantii at the chromosome level using a combination of long Nanopore reads from sequencing with high-throughput chromosome conformation capture technology. When finally assembled, the genome was 318.95 Mb on four chromosomes with a 15.19 Mb scaffold N50. A total of 12,162 genes encoded proteins, while there were 22.01% repetitive sequences that totaled 67.73 Mb. Phylogenetic analyses revealed that T. aurantii and Aphis gossypii parted ways approximately 7.6 million years ago (Mya). We used a combination of long-read single-molecule sequencing with Hi-C-based chromatin interaction maps that resulted in a reference chromosomal level reference genome of T. aurantii that was high quality. Our results will enable the exploration of the genetics behind the special biological features of T. aurantii and also provide a source of data that should be useful to compare the compare genome among the Hemiptera.
橘蚜（半翅目：蚜科）能侵袭多种植物寄主，包括茶树（茶）、柑橘（柑橘属）、荔枝（荔枝）、香蕉（芭蕉属）和菠萝（凤梨）等。它是一种分布广泛的六足动物，也是茶园中最具破坏性的害虫之一，每年给茶叶生产造成巨大经济损失。高质量的参考基因组对于研究橘蚜的系统发育和进化很重要，因为其基因组高度杂合且重复。我们结合长读长的纳米孔测序数据和高通量染色体构象捕获技术，获得了染色体水平的橘蚜从头基因组组装。最终组装完成时，基因组在四条染色体上共318.95 Mb，支架N50为15.19 Mb。总共12162个基因编码蛋白质，同时有22.01%的重复序列，总计67.73 Mb。系统发育分析表明，橘蚜和棉蚜大约在760万年前分道扬镳。我们结合长读长单分子测序和基于Hi-C的染色质相互作用图谱，得到了高质量的橘蚜参考染色体水平参考基因组。我们的结果将有助于探索橘蚜特殊生物学特性背后的遗传学，也为半翅目之间的基因组比较提供有用的数据来源。
