Improved Apis mellifera reference genome based on the alternative long-read-based assemblies.

Area of Science:

• Genomics
• Zoology
• Bioinformatics

Background:

• The western honey bee (Apis mellifera L.) is crucial for crop pollination and serves as a model organism for social behavior studies.
• Existing honey bee genome assemblies have limitations, including numerous gaps, unplaced scaffolds, and missing telomeres, particularly in repetitive regions.

Purpose of the Study:

• To improve the quality of the western honey bee reference genome by resolving assembly gaps and adding missing telomeres.
• To enhance the accuracy of genomic resources for Apis mellifera L. to support future research.

Main Methods:

• Utilized de novo re-assemblies from raw reads of the Amel_HAv_3.1 reference genome and other long-read assemblies.
• Employed PacBio read mapping and gene annotation assessment to validate the accuracy of the corrected assembly.
• Focused on resolving gaps, unplaced scaffolds, and telomeres within highly repetitive chromosomal regions.

Main Results:

• Successfully resolved 13 gaps, five unplaced/unlocalized scaffolds, and two distal telomeres in the Amel_HAv_3.1 assembly, totaling 848,747 bp.
• Identified consistent assembly failures in highly repetitive regions across different PacBio-read-based assemblies, notably on chromosome 10.
• The updated assembly provides a more accurate resource for reference-guided scaffolding and marker mapping.

Conclusions:

• The study significantly improved the western honey bee genome assembly by addressing limitations in repetitive regions.
• While improvements were made, ultra-long Nanopore sequencing may be necessary for complete resolution of complex repetitive regions.
• The enhanced genome assembly facilitates more accurate and reliable honey bee genomics studies.