Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual

Wei Liu, Qiang Lin, Qi Wang, Wanfei Liu, Jing Jia, Jie Zhang, Ling Yang, Yongyue Lu, Peng Cui () and Guirong Wang ()
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Wei Liu: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen
Qiang Lin: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen
Qi Wang: Northeast Forestry University, School of Forestry, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education
Wanfei Liu: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen
Jing Jia: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen
Jie Zhang: HuBei Min Zu University, Hubei Key Laboratory of Biological Resources Protection and Utilization, College of Forestry and Horticulture
Ling Yang: Shanxi Agricultural University, College of Forestry
Yongyue Lu: South China Agricultural University, Department of Entomology
Peng Cui: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen
Guirong Wang: Chinese Academy of Agricultural Sciences, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract Dipteran insects include numerous harmful species that cause significant agricultural damage. However, assembly of genomes for species in this order has been difficult due to their small body size, poor conservation of telomere and centromere structures, high levels of heterozygosity, and complex genetic backgrounds. In this study, we assemble a high-quality 596 Mb telomere-to-telomere genome for Bactrocera dorsalis, a fruit crop pest, using a strategy with a low-input HiFi CCS library from a male individual and an ONT sequence from pooled inbred individuals. The assembly includes complete structural organization information for centromeres and telomeres, providing insights into the evolution of chromosome structure in insects. Comparative genomic analysis reveals the polyphyletic origin of sex chromosomes across Diptera. Furthermore, we identify a homolog of ATPsynβ as a Y chromosome-specific gene that is highly expressed across multiple male tissues and may provide critical support for male-specific physiological activities. Additionally, we discover several tandem duplications of odorant receptor genes, including a triplet of the OR88a family, which was validated to be involved in the behavioral response to methyl eugenol. In summary, this complete reference genome provides a foundation for future genomic research in Diptera and offers genetic insights for the control of B. dorsalis.

Date: 2025
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DOI: 10.1038/s41467-025-65870-1

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