Volume 45 Issue 1
Jan.  2024
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Yu-Ran Li, Zheng-Wei Wang, Richard T. Corlett, Wen-Bin Yu. Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini. Zoological Research, 2024, 45(1): 160-175. doi: 10.24272/j.issn.2095-8137.2023.169
Citation: Yu-Ran Li, Zheng-Wei Wang, Richard T. Corlett, Wen-Bin Yu. Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini. Zoological Research, 2024, 45(1): 160-175. doi: 10.24272/j.issn.2095-8137.2023.169

Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

doi: 10.24272/j.issn.2095-8137.2023.169
The newly sequenced and assembled mitogenomes of Meliponini can be downloaded from NCBI (accession numbers in Supplementary Table S4). All the newly assembled mitogenomes can be downloaded from China National Center for Bioinformation (Supplementary Table S5) (PRJCA021965) and Science Data Bank databases (DOI: 10.57760/sciencedb.j00139.00088).
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
W.B.Y., R.T.C., and Y.R.L. conceived and designed the research; Z.W.W. and Y.R.L. collected and identified samples; Y.R.L. and W.B.Y. analyzed the data and interpreted results; Y.R.L. and W.B.Y. wrote draft of the manuscript; all authors revised and approved the final version of the manuscript.
Funds:  This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), Science and Technology Basic Resources Investigation Program of China (2021FY100200), Yunnan Revitalization Talent Support Program “Young Talent” and "Innovation Team" Projects, and the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science (XTBG-1450101)
More Information
  • The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.
  • The newly sequenced and assembled mitogenomes of Meliponini can be downloaded from NCBI (accession numbers in Supplementary Table S4). All the newly assembled mitogenomes can be downloaded from China National Center for Bioinformation (Supplementary Table S5) (PRJCA021965) and Science Data Bank databases (DOI: 10.57760/sciencedb.j00139.00088).
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    W.B.Y., R.T.C., and Y.R.L. conceived and designed the research; Z.W.W. and Y.R.L. collected and identified samples; Y.R.L. and W.B.Y. analyzed the data and interpreted results; Y.R.L. and W.B.Y. wrote draft of the manuscript; all authors revised and approved the final version of the manuscript.
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