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. 2025 Mar 5;12(1):386.
doi: 10.1038/s41597-025-04711-8.

Chromosome-level genome assembly of soybean aphid

Shaolong Qiu #  1 , Ningning Wu #  1 , Xiaodong Sun #  2 , Yongguo Xue  3 , Jixing Xia  4
Affiliations

Chromosome-level genome assembly of soybean aphid

Shaolong Qiu et al. Sci Data. .

Abstract

Soybean aphid (Aphis glycines) is one of the main pests on soybeans, which causes serious damage to the soybean worldwide. The current genome of the soybean aphid is quite fragmented, which has impeded scientific research to some extent. In this study, we assembled a chromosome-level genome of the soybean aphid using MGI short reads, PacBio HiFi long reads and Hi-C reads. The genome sequence was anchored to four pseudo-chromosomes, with a total genome length of 324 Mb and a scaffold N50 length of 88.85 Mb. We evaluated the genome based on insecta_odb10 and the results show it has a completeness of 97.2%. A total of 20,781 protein-coding genes were predicted in the genome, of which 17,183 genes were annotated in at least one protein database. Our work provides a new genomic resource for the soybean aphid study.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The characteristics of A. glycines genome estimated using k-mer distribution (k = 21).
Fig. 2
Fig. 2
Genome-wide Hi-C heatmap and circos plot of the A. glycines Genome. (a) The Hi-C contact heatmap of the A. glycines genome. The boundary indicates that the genome contains four chromosomes. (b) The circos plot of the A. glycines genomic features. The four tracks represent chromosome length, repeat density, gene density and GC density from the outermost to the innermost. The window size was defined as 100 kb.
Fig. 3
Fig. 3
Genome synteny analyses of A. glycines and two aphids. (a) Genome synteny analysis between A.gly and A.pis. (b) Genome synteny analysis between A.gly and E.lan. A.gly refers to A. glycines, A.pis refers to A. pisum and E.lan refers to E. lanigerum.
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