Complete mitochondrial genome of Bombus terrestris (Hymenoptera: Apidae)

Genus-Wide Characterization of Nuclear Mitochondrial DNAs in Bumblebee (Hymenoptera: Apidae) Genomes

Simple Summary

The DNA of mitochondria can be transferred into the nucleus and form nuclear mitochondrial DNAs (NUMTs). In this study, we identified and characterized NUMTs in genus-wide bumblebee species. The number of NUMTs in bumblebee is much lower than those in its closely related taxon, honeybee. The insertion sites of NUMTs in bumblebee are not random, with AT-rich regions harboring more NUMTs. In addition, NUMTs derived from the mitochondrial COX1 gene are most abundant in the nuclear genome. While the majority of NUMTs seem unfunctional in the bumblebee, some NUMTs show functional clues, which could fuse with their flanking sequences to form novel proteins. Our results shed light on the molecular features of NUMTs and uncover their contribution to genome innovation in the bumblebee.

Abstract

In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation.

Next-generation sequencing of the mitochondrial genome of Bombus longipennis Friese, 1918 (Hymenoptera: Apidae)

Bombus longipennis is the species of Bumblebees (Hymenoptera: Apidae), which are important pollinators for wild plants and greenhouses crops. The complete mitochondrial genome (mitogenome) of B. longipennis was determined by next-generation sequencing. The mitogenome was 18,458 bp in size with 87.2% A + T content, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an AT-rich control region (D-loop). Gene arrangement was found to be identical to those of other mitogenomes of bumblebees (e.g. Bombus terrestris and Bombus ignitus). All 13 PCGs initiated with typical ATN codons. Among them, 11 PCGs terminated with TAA or TAG; only cox2 and nad4 have incomplete stop codon T. All 22 tRNAs can be folded into typical cloverleaf structure. Phylogenetic analysis based on the concatenated nucleotide sequences of all 13 PCGs indicated that B. longipennis was more closely related to other species of subgenus Bombus, which clustered into a monophyletic group.

The complete mitochondrial genome of Bombus filchnerae (Hymenoptera: Apidae) and phylogenetic analysis

Here, we report the complete mitochondrial genome (mitogenome) of Bombus filchnerae (Hymenoptera: Apidae). The genome size of B. filchnerae was 18,553 bp with 88.7% A + T content, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an AT-rich control region (D-loop). tRNA rearrangement was observed in this mitochondrial genome when compared to those of other bumblebee species (e.g. Bombus breviceps and Bombus asiaticus). All the 13 PCGs initiated with typical ATN codons. Among them, 11 PCGs terminated with TAA, only nad4 and nad5 with incomplete stop codon TA and T, respectively. All the 22 tRNAs can be folded into typical cloverleaf structure, except for trnS1, whose dihydrouridine (DHU) arm forms a simple loop. The phylogenetic analysis based on the concatenated nucleotide sequences of all 13 PCGs indicated that B. filchnerae showed the closest relationship with Bombus pascuorum, forming a mono clade of the subgenus Thoracobombus, with well-resolved relationships among nine Bombus subgenera.

The complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae) from Hokkaido Island, Japan

The complete is mitochondrial genome of the Japanese bumblebee Bombus hypocrita sapporensis from Hokkaido Island, Japan is analysed using next generation sequencing. The mitochondrial genome of B. h. sapporensis was observed to be a circular molecule of 15,835 bp. The average AT content in the B. h. sapporensis mitochondrial genome was 85.53%. It was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The PCGs had ATA, ATG, or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE, trnF, and trnS1. The molecular phylogenetic analysis indicated that the B. h. sapporensis from Hokkaido Island population was most similar to that of the geographically isolated B. h. sapporensis from Rebun Island.

Proteomic Characterization of the Venom of Five Bombus (Thoracobombus) Species

Venomous animals use venom, a complex biofluid composed of unique mixtures of proteins and peptides, to act on vital systems of the prey or predator. In bees, venom is solely used for defense against predators. However, the venom composition of bumble bees (Bombus sp.) is largely unknown. The Thoracobombus subgenus of Bombus sp. is a diverse subgenus represented by 14 members across Turkey. In this study, we sought out to proteomically characterize the venom of five Thoracobombus species by using bottom-up proteomic techniques. We have obtained two-dimensional polyacrylamide gel (2D-PAGE) images of each species’ venom sample. We have subsequently identified the protein spots by using matrix assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS). We have identified 47 proteins for Bombus humilis, 32 for B. pascuorum, 60 for B. ruderarius, 39 for B. sylvarum, and 35 for B. zonatus. Moreover, we illustrated that intensities of 2DE protein spots corresponding to putative venom toxins vary in a species-specific manner. Our analyses provide the primary proteomic characterization of five bumble bee species’ venom composition.

Complete mitochondrial genome of Bombus consobrinus (Hymenoptera: Apidae)

The complete mitochondrial genome of Bombus consobrinus was sequenced. This circular mitogenome is 17,966 bp (86.7% of AT) in length, which contains 22 tRNA genes, 13 protein-coding genes and two rRNA genes. All protein-coding genes are initiated with the typical ATN codon and terminated by TAA codon except an incomplete stop codon T for ND4 gene. tRNA-Ser (AGN) lacks a dihydrouridine (DHU) arm while other tRNA genes form a typical cloverleaf structure. The complete mitochondrial genome of B. consobrinus will be useful to understand the inter-species relationship and genetic diversity of bumblebees.

Complete mitochondrial genome of Bombus breviceps (Hymenoptera: Apidae)

The complete mitochondrial genome of Bombus breviceps, which belongs to the subgenus of Alpigenobombus in Bombus genus, was sequenced. This circular mitogenome is 16,743 bp (83.5% AT) in length, with two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. All protein-coding genes are initiated with the common invertebrate initiation codon except TTA for ND2, and terminated by the typical stop codon TAA or TAG. tRNA-Ser (TCT) lacks a dihydrouridine (DHU) arm while other tRNA genes form a cloverleaf structure. Phylogenetic analysis shows that genus Bombus has a closer relationship with genus Melipona than any other genera in Apidae family, and B. breviceps clusters closer to B. lapidarius than any other bumblebees with sequenced mitogenome.

Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita hypocrita (Insecta: Hymenoptera: Apidae)

In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.

Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae)

In the present study, we describe the complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis from the Rebun Island, in Hokkaido, Japan. The mitochondrial genome of B. hypocrita sapporensis includes a circular molecule of 15 700 bp. It contains 13 protein-coding genes, 22 tRNA genes, two rDNA genes and an A + T-rich control region. All protein-coding genes are initiated by ATA, ATG, and ATT codons and are terminated by the typical stop codon TAA or T, except for ND4L, which ends with TA. All tRNA genes typically form a cloverleaf secondary structure.