Complete mitochondrial genome sequence of Melipona scutellaris, a Brazilian stingless bee

Mitochondrial genome of the mason bee, Osmia pedicornis (Hymenopetra: Megachilidae)

The mason bee, Osmia pedicornis Cockerell, 1919, which is importantly used as the pollinator, particularly for apples in Korea. We sequenced the mitochondrial genome (mitogenome) of O. pedicornis as an initial study for species identification and subsequent population genetic study. The size of the incomplete genome was 14,505 bp, excluding the trnA, trnC, and the A + T-rich region that were unable to sequence, but including partially sequenced trnM and srRNA. The genome included typical sets of protein-coding genes (PCGs), rRNA genes, and one non-coding region, tRNAs, excluding two unidentified tRNAs. Although positions of the two tRNAs that were not sequenced are unknown the gene arrangement of O. pedicornis mitogenome has the tRNA arrangement, trnM-trnQ-trnI, at the A + T-rich region and ND2 junction that differed from that of previously published O. excavate, which has trnA-trnQ-trnI arrangement at the junction. Phylogenetic analyses were performed using concatenated sequences of the 13 PCGs genes and the maximum likelihood method with the inclusion of a total of 12 mitogenome sequences belonging to three families in the superfamily Apoidea. Current O. pedicornis was placed as the sister to the O. bicornis, with the highest nodal support. The Apidae and Megachilidae were placed as the sister group, with the placement of Colletidae as the basal lineage for the group with the highest nodal support.

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

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.