The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste

Abstract

Background Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. Results The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. Conclusions The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.

First Draft Genome Assembly of the Malaysian Stingless Bee, Heterotrigona itama (Apidae, Meliponinae)

“…In addition, the genome was found to be slightly repetitive, and the estimated genome size of the Malaysian stingless bee (H. itama) was discovered to be approximately 272 Mb. This is similar to the size of previously reported genomes of the honey bee (Apis mellifera-236 Mb) [18], bumble bee (Bombus terrestris-249 Mb) [19] and two Neotropical stingless bee species (M. quadrifasciata-256 Mb, F. varia-275 Mb) [15,16]. Based on the draft genome size estimated, subsequent de novo assembly and genome annotation were performed with the sequencing depth of approximately 49X coverage.…”

“…In addition, the data can be useful as a genomic reference to facilitate future studies on sustainable cultivation and conservation of stingless bees. The sequenced H. itama genome is the first report for the Indo-Malayan/Australasian stingless bee group and the fourth in the world after two Neotropical stingless bees, Melipona quadrifasciata and Frieseomelitta varia [15,16], and an Asian species from Taiwan, Lepidotrigona ventralis hoosana (GenBank accession: PRJNA387986), which had been revised as Lepidotrigona hoozana (Strand) Rasmussen [1].…”

Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera

“…Living in large colonies with one monandrous queen, F. varia workers are completely sterile with heavily modified and non-functional ovaries [ 50 ]. The genome of F. varia has been sequenced and assembled [ 55 ]. Hence, we chose F. varia to construct a high-quality recombination map using SNP markers, benefitting from recent advances in sequencing technology and the large number of haploid sons produced by a single female in this species.…”

10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees

“…Concerning stingless bees, works on their epigenetics remain limited. Recently, a complete set of genes involved in DNA methylation and in histone post-translational modifications in the genome of Frieseomellita varia was reported 47 . Moreover, in our previous studies, we demonstrated a functional methylation/demethylation system as well as post-translational modifications of histones in the stingless bee Melipona scutellaris .…”