Insights from Melipona bicolor hybrid genome assembly: a stingless bee genome with chromosome-level scaffold

Abstract

Background The highly eusocial stingless bees are crucial pollinators of native and agricultural ecosystems. Nevertheless, genomic studies within this bee tribe remain scarce. We present the genome assembly of the stingless bee Melipona bicolor. This bee is a remarkable exception to the typical single-queen colony structure, since in this species, multiple queens may coexist and share reproductive duties, resulting in genetically diverse colonies with weak kinship connections. As the only known genuinely polygynous bee, M. bicolor’s genome provides a valuable resource for investigating sociality beyond kin selection. Results The genome was assembled employing a hybrid approach combining short and long reads, resulting in 241 contigs spanning 259 Mb (N50 of 6.2 Mb and 97.5% complete BUSCOs). Comparative analyses shed light on some evolutionary aspects of stingless bee genomics, including multiple chromosomal rearrangements in Melipona. Additionally, we explored the evolution of venom genes in M. bicolor and other stingless bees, revealing that, apart from two genes, the conserved repertoire of venom components remains under purifying selection in this clade. Conclusion This study advances our understanding of stingless bee genomics, contributing to the conservation efforts of these vital pollinators and offering insights into the evolutionary mechanisms driving their unique adaptations.

The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics

“…This may be due to an unusually large repetitive content—62.8 Mb or 22.1% of the genome—even in comparison with that of F. varia (39.1 Mb or 14.2% of the genome) [ 24 ]. The number of protein-coding genes found in the genome of T. angustula (17,458) is also higher than previously predicted for the stingless bee species sequenced so far, except M. bicolor (20,278 protein-coding genes), although this number may be overestimated [ 113 ]. Moreover, none of the other stingless bee genomes sequenced to date was annotated using transcriptomic evidence from multiple life stages as in the present study.…”

“…The use of LRs in the present study exemplifies how this technology can result in higher assembly quality metrics, when compared to previous stingless bee genomes assembled based only on SRs (Supplementary Table S14 ). On the other hand, the same metrics were not as performant as the ones from the LR-assembled genomes of M. bicolor and other eusocial bees [ 113 – 115 ]. One possible explanation for these results is that we could only generate 2.31 Gb worth of LRs, which resulted in a low sequencing coverage (8-fold).…”

“…Moreover, none of the other stingless bee genomes sequenced to date was annotated using transcriptomic evidence from multiple life stages as in the present study. It is nevertheless important to ponder that the procedures adopted for repeat masking and gene prediction herein and previously differed considerably [ 18 , 24 , 113 ], meaning that direct comparisons must be interpreted with caution.…”