State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
G3 (Bethesda). 2024 Nov 6;14(11). doi: 10.1093/g3journal/jkae223.
The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.
甘蔗绵蚜，麦长管蚜，是一种农业害虫，会对禾本科（草类）植物，如高粱和甘蔗，造成损害。在本研究中，我们使用纳米孔长读和高通量染色体构象捕获染色质互作图谱，生成了一个染色体水平的组装，总长度为 356.1Mb，其中 85.5%（304.6Mb）包含在 3 条常染色体和 X 染色体中。重复序列占染色体的 16.29%，共注释了 12530 个蛋白编码基因，达到了 95.8%的基准通用单拷贝直系同源基因完整性。与之前低质量的基因组资源相比，这有了显著的提高。通过将 M. sacchari 与代表 3 个蚜虫部落的 24 个已发表的蚜虫基因组进行比较的系统发生基因组分析表明，M. sacchari 属于蚜虫部落 Aphidini，并与其他 Aphidini 物种保持保守的染色体结构。本研究中报告的高质量基因组资源有助于理解蚜虫基因组的进化和研究 M. sacchari 的害虫管理。
