Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY G3: Genes|Genomes|Genetics Pub Date : 2024-09-18 DOI:10.1093/g3journal/jkae223

Jinshuai Zhao, Liqiang Xie, Xinrui Zhao, Luhua Li, Jianghui Cui, Jinfeng Chen

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Abstract

The sugarcane aphid, Melanaphis sacchari (Zehntner, 1897), is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. Here, we used Nanopore long reads and Hi-C interaction map 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 three 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 orthologs (BUSCO) gene completeness. This offers a substantial improvement compared to previous low-quality genomic resources. Phylogenomic analysis by comparing M. sacchari with twenty-four published aphid genomes representing three aphid tribes reveals that M. sacchari belongs to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study will be useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.

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甘蔗蚜虫 Melanaphis sacchari（半翅目：蚜科）的基因组序列

甘蔗蚜（Melanaphis sacchari (Zehntner, 1897)）是一种农业害虫，主要危害高粱和甘蔗等禾本科植物。在这里，我们利用 Nanopore 长读数和 Hi-C 交互图谱生成了染色体级的装配，总长度为 356.1 Mb，其中 85.5% （304.6 Mb）包含在三个常染色体和 X 染色体中。重复序列占染色体的 16.29%，共注释了 12,530 个编码蛋白质的基因，实现了 95.8% 的基准通用单拷贝同源物（BUSCO）基因完整性。这与之前的低质量基因组资源相比有了大幅提高。通过将M. sacchari与已发表的代表三个蚜虫部落的24个蚜虫基因组进行系统进化分析，发现M. sacchari属于蚜虫部落，并与其他蚜虫物种保持着保守的染色体结构。这项研究报告的高质量基因组资源将有助于了解蚜虫基因组的进化和研究囊蚜的害虫管理。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.