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The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae)

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Abstract

The complete mitochondrial genome (mitogenome) of the sawfly, Nesodiprion zhejiangensis Zhou & Xiao, was sequenced, assembled, and deposited in GenBank (Accession Number: OM501121). The 15,660 bp N. zhejiangensis mitogenome encodes for 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and an AT-rich region of 450 bp in length. The nucleotide composition is biased toward adenine and thymine (A + T = 81.8%). Each PCG is initiated by an ATN codon, except for cox2, which starts with a TTG. Of 13 PCGs, 9 have a TAA termination codon, while the remainder terminate with a TAG or a single T. All tRNAs have the classic cloverleaf structure, except for the dihydrouridine (DHU) arm of tRNAval, which forms a simple loop. There are 49 helices belonging to 6 domains in rrnL and 30 helices belonging to 4 domains in rrnS. In comparison to the ancestral architecture, N. zhejiangensis has the most rearranged mitogenome in Symphyta, in which rearrangement events of local inversion and transposition are identified in three gene clusters. Specifically, the main hotspot of gene rearrangement occurred between rrnS and trnY, and rearranged from rrnS-(AT-rich region)-I-Q-M-nd2-W–C-Y to rrnS-Q-W–C-nd2-I-M-(AT-rich region)-Y, involving a local inversion event of a large gene cluster and transposition events of some tRNAs. Transposition of trnA and trnR (rearranged from A-R to R-A) was observed at the nd3-nd5 gene junction while shuffling of trnP and trnT (rearranged from T-P to P–T) occurred at the nd4l-nd6 gene junction. While illegitimate inter-mtDNA recombination might explain the opposite orientations of transcription between rrnS and trnY, transposition events of tRNA in some gene blocks can be accounted for by the tandem duplication/random loss (TDRL) model. Our phylogenetic analysis suggests that N. zhejiangensis is closely related to congeneric species N. biremis and N. japonicus, which together form a sister lineage with the European pine sawfly, Neodiprion sertifer.

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Data availability

The data that support the findings of this study are openly available in the NCBI GenBank at https://www.ncbi.nlm.nih.gov under the accession number OM501121. The associated BioProject, SRA, and BioSample numbers are PRJNA803467, SRR17888682, and SAMN25652947, respectively.

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Acknowledgements

The authors are grateful to anonymous reviewers for their constructive comments and suggestions. Special thanks go to Hu Li (China Agricultural University) for his insights into the organization and architecture of insect mitochondrial genomes.

Funding

This research was supported by the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (Grant Number: CAFYBB2018QB005; CAFYBB2018GB001), the Beijing Municipal Science and Technology Project (Z201100008020001) and the National Key Research and Development Program of China (Grant number: 2018YFD0600202).

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Authors and Affiliations

  1. Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China

    Chao Bai, Danjie Xie, Jie Cao & Qinghua Wang

  2. Beijing Xinhai Garden Engineering Co., LTD, Beijing, China

    Chao Bai & Jie Cao

  3. College of Plant Protection, China Agricultural University, Beijing, China

    Yunfei Wu

  4. Department of Entomology, University of Kentucky, Lexington, KY, USA

    Austin Merchant, Qinghua Wang & Xuguo Zhou

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  1. Chao Bai
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  2. Yunfei Wu
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  3. Austin Merchant
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  4. Danjie Xie
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  5. Jie Cao
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  6. Qinghua Wang
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Contributions

X.Z. and Q.H.W. designed the experiments; C.B. and J.C. carried out the research; Q.H.W. and D.X. contributed reagents/materials/analysis tools; Q.H.W. and Y.F.W analyzed the data; Q.H.W. and A.M. drafted the manuscript, X.Z. and Y.F.W. revised the manuscript. All authors gave the final approval for publication.

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Correspondence to Qinghua Wang or Xuguo Zhou.

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Bai, C., Wu, Y., Merchant, A. et al. The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae). Funct Integr Genomics 23, 41 (2023). https://doi.org/10.1007/s10142-022-00959-0

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