Retroelement expansions underlie genome evolution in stingless bees.

Area of Science:

• Insect genomics
• Evolutionary biology
• Eusocial insect genetics

Background:

• Stingless bees (Melipona) exhibit distinct heterochromatin organization, correlating with genome size and transposable element (TE) content.
• Understanding these differences is key to exploring genome evolution in insects.

Purpose of the Study:

• To provide high-resolution genome assemblies for two Melipona species with contrasting heterochromatin content.
• To investigate the role of TEs in shaping genome structure and heterochromatin distribution.

Main Methods:

• Long-read sequencing and 3D chromosome conformation scaffolding for genome assembly.
• Comparative genomic analyses of M. quadrifasciata and M. scutellaris.
• Analysis of transposable element content, distribution, and association with structural variants.

Main Results:

• Genome assemblies reveal conserved synteny but significant divergence in structural variants and TE types between the two species.
• M. scutellaris shows an expansion of retrotransposons (Gypsy/DIRS1) in TE hotspots linked to rearrangements.
• Distinct methylation patterns and expanded histone deacetylase orthologs observed in M. scutellaris.
• TE dynamics, with retrotransposon expansion in M. scutellaris and DNA transposon expansion in M. quadrifasciata, explain heterochromatin differences despite similar genome sizes.

Conclusions:

• Transposable element dynamics are a major driver of heterochromatin variation and chromosomal evolution in Melipona.
• TEs significantly influence epigenetic innovation and genome structural diversity in eusocial insects.
• High-resolution genomic resources for these species advance understanding of genome evolution in stingless bees.