Chromosome level de Novo hybrid assembly of Asian honeybee, Apis cerana Koreana

Chromosome level de Novo hybrid assembly of Asian honeybee, Apis cerana Koreana

Abstract Apis cerana is a vital pollinator in East Asia and a model species for studying eusociality, which includes complex group decision-making and specialized task systems. However, the population of Apis cerana is facing a significant decline globally due to factors such as excessive pesticide...

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Bibliographic Details
Main Authors: Jeong-Hyeon Lee, Byung-Ju Kim, Giyoun Han, Olga Frunze, Gyongju Nah, Hyung Wook Kwon
Format: Article
Language:English
Published: Nature Portfolio 2025-07-01
Series:Scientific Reports
Subjects:
Chromosome-level assembly
Oxford nanopore sequencing
Hybrid method
Apis cerana
Whole genome sequencing
Online Access:https://doi.org/10.1038/s41598-025-12338-3
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Summary:Abstract Apis cerana is a vital pollinator in East Asia and a model species for studying eusociality, which includes complex group decision-making and specialized task systems. However, the population of Apis cerana is facing a significant decline globally due to factors such as excessive pesticide use, climate change, and infectious diseases. Comprehensive genomic resources are crucial for preserving this species and understanding the genomic underpinnings of eusociality. In this study, we present a near-complete de novo assembly of the Apis cerana genome, designated AcerK1.0, achieved using a hybrid assembly approach combining nanopore long-read and Illumina short-read sequencing technologies. The final assembly comprises approximately 223 Mbp, including 16 chromosomes (217 Mbp), four unmapped scaffolds (6 Mbp), a mitochondrial sequence of 15,890 bp, and 12 gaps totaling 503 Ns. Comparative analyses against existing assemblies using metrics such as N50, Benchmarking Universal Single-Copy Orthologs (BUSCO) on hymenoptera dataset, and RNA-seq coverage indicate significant improvements in genome quality, validating AcerK1.0 as a reference-grade assembly. The AcerK1.0 genome represents a valuable resource for understanding the genetic diversity of Apis cerana and advancing research on eusocial traits through genomic approaches. The raw sequence reads are available in the NCBI Short Read Archive under project PRJNA779817 (SRR17574130), and the final genome assembly has been deposited in the NCBI Assembly database (accession number GCA_029169275.1).
ISSN:2045-2322

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