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The Complete Mitochondrial Genome of Lepidotrigona flavibasis (Hymenoptera: Meliponini) and High Gene Rearrangement in Lepidotrigona Mitogenomes.

ABSTRACT: We reported the sequence and characteristics of the complete mitochondrial genome of an ecologically important stingless bee, Lepidotrigona flavibasis (Hymenoptera: Meliponini), that has suffered serious population declines in recent years. A phylogenetic analysis based on complete mitogenomes indicated that L. flavibasis was first clustered with another Lepidotrigona species (L. terminata) and then joined with the other two Melipona (Hymenoptera: Meliponini) stingless bees (M. scutellaris and M. bicolor), forming a single clade of stingless bees. The stingless bee clade has a closer relationship with bumblebees (Bombus) (Hymenoptera: Apidae) than with honeybees (Apis) (Hymenoptera: Apidae). Extremely high gene rearrangements involving tRNAs, rRNAs, D-loop regions, and protein-coding genes were observed in the Lepidotrigona mitogenomes, suggesting an overactive evolutionary status in Lepidotrigona species. These mitogenomic organization variations could provide a good system with which to understand the evolutionary history of Meliponini.

SUBMITTER: Wang CY

PROVIDER: S-EPMC8174572 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtusplautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O.plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioiacunea and calculated the Ka/Ks ratio for each set of PCGs. The highest value of the Ka/Ks ratio within 13 PCGs was found in nad2 with 1.1, suggesting that they were subjected to positive selection. This phenomenon was first discovered in Encyrtidae. Compared with other encyrtid mitogenomes, a translocation of trnW was found in O.plautus, which was the first of its kind to be reported in Encyrtidae. Comparing with ancestral arrangement pattern, wasps reflect extensive gene rearrangements. Although these insects have a high frequency of gene rearrangement, species from the same family and genus tend to have similar gene sequences. As the number of sequenced mitochondrial genomes in Chalcidoidea increases, we summarize some of the rules of gene rearrangement in Chalcidoidea, that is four gene clusters with frequent gene rearrangements. Ten mitogenomes were included to reconstruct the phylogenetic trees of Encyrtidae based on both 13 PCGs (nucleotides of protein coding genes) and AA matrix (amino acids of protein coding genes) using the maximum likelihood and Bayesian inference methods. The phylogenetic tree reconstructed by Bayesian inference based on AA data set showed that Aenasiusarizonensis and Metaphycuseriococci formed a clade representing Tetracneminae. The remaining six species formed a monophyletic clade representing Encyrtinae. In Encyrtinae, Encyrtus forms a monophyletic clade as a sister group to the clade formed by O.plautus and Diaphorencyrtusaligarhensis. Encyrtussasakii and Encyrtusrhodooccisiae were most closely related species in this monophyletic clade. In addition, gene rearrangements can provide a valuable information for molecular phylogenetic reconstruction. These results enhance our understanding of phylogenetic relationships among Encyrtidae.

Dataset Information

The Complete Mitochondrial Genome of Lepidotrigona flavibasis (Hymenoptera: Meliponini) and High Gene Rearrangement in Lepidotrigona Mitogenomes.

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