close
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb 9;13(2):e9813.
doi: 10.1002/ece3.9813. eCollection 2023 Feb.

The mitochondrial genomes of the Geometroidea (Lepidoptera) and their phylogenetic implications

Weili Ding  1 , Haizhen Xu  2 , Zhipeng Wu  2 , Lizong Hu  2 , Li Huang  2 , Mingsheng Yang  2 , Lili Li  2   3
Affiliations

The mitochondrial genomes of the Geometroidea (Lepidoptera) and their phylogenetic implications

Weili Ding et al. Ecol Evol. .

Abstract

The Geometroidea is a large superfamily of Lepidoptera in species composition and contains numerous economically important pest species that cause great loss in crop and forest production. However, understanding of mitogenomes remains limited due to relatively fewer mitogenomes previously reported for this megadiverse group. Here, we sequenced and annotated nine mitogenomes for Geometridae and further analyzed the mitogenomic evolution and phylogeny of the whole superfamily. All nine mitogenomes contained 37 mitochondrial genes typical in insects, and gene organization was conserved except for Somatina indicataria. In S. indicataria, the positions of two tRNAs were rearranged. The trnR was located before trnA instead of after trnA typical in Lepidoptera, whereas the trnE was detected rarely on the minority strand (N-strand). This trnR-trnA-trnN-trnS1-trnE-trnF newly recognized in S. indicataria represents the first gene rearrangement reported for Geometroidea and is also unique in Lepidoptera. Besides, nucleotide composition analyses showed little heterogeneity among the four geometrid subfamilies involved herein, and overall, nad6 and atp8 have higher nucleotide diversity and Ka/Ks rate in Geometridae. In addition, the taxonomic assignments of the nine species, historically defined by morphological studies, were confirmed by various phylogenetic analyses based on the hitherto most extensive mitogenomic sampling in Geometroidea.

Keywords: Geometridae; gene rearrangement; mitochondrial genome; phylogeny.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Circular diagram of the nine mitogenomes sequenced in this study. Different color is marked to show the nucleotide identity of BLAST hits relative to the reference mitogenome of Somatina indicataria at the outer circle.
FIGURE 2
FIGURE 2
Gene arrangements of reported lepidopteran mitogenomes relative to ancestral insect mitogenome. Red rectangles indicate the two gene clusters with gene rearrangement. The gene with underline is located on the N‐strand. The taxon and its classification with gene rearrangement reported in this study are marked in bold.
FIGURE 3
FIGURE 3
Nucleotide composition of the geometrid mitogenomes. (a) A + T content. (b) AT skew. (c) The averaged effective number of codons (ENC) of four geometrid subfamilies. (d) Scatter plot of the GC content of 3rd codon sites versus ENC.
FIGURE 4
FIGURE 4
Gene variation of 13 PCGs in Geometridae. (a) The sliding window analysis shows the value of nucleotide diversity. (b) The Ka, Ks, and Ka/Ks of each PCG among geometrid representatives. Ka—nonsynonymous substitution; Ks—synonymous substitution.
FIGURE 5
FIGURE 5
Maximum likelihood (ML) tree inferred from IQ‐TREE method based on PCG123R dataset. The species with newly sequenced mitogenome is emphasized in bold. Numbers separated by slash (/) on node represent the bootstrap values based on the PCG123R, PCG123, PCG12R, PCG12, and PCGAA datasets, respectively. The “*” on node represents bootstrap values ≥90 for all datasets. The “‐” represents an unrecovered node in ML tree of the corresponding dataset.
FIGURE 6
FIGURE 6
Bayesian tree inferred from MrBayes method based on PCG123R dataset. The species with newly sequenced mitogenome is emphasized in bold. Numbers separated by slash (/) on node represent the posterior probabilities based on the PCG123R, PCG123, PCG12R, PCG12, and PCGAA datasets, respectively. The “*” on node represents posterior probabilities ≥0.95 for all datasets. The “‐” represents unrecovered node in Bayesian tree of corresponding dataset.
See this image and copyright information in PMC

References

    1. Abascal, F. , Zardoya, R. , & Telford, M. J. (2010). TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research, 38, 7–13. - PMC - PubMed
    1. Bazinet, A. L. , Cummings, M. P. , Mitter, K. T. , & Mitter, C. (2013). Can RNA‐seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS One, 8, e82615. - PMC - PubMed
    1. Boore, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767–1780. - PMC - PubMed
    1. Cameron, S. L. (2014). Insect mitochondrial genomics: Implications for evolution and phylogeny. Annual Review of Entomology, 59, 95–117. - PubMed
    1. Cameron, S. L. , & Whiting, M. F. (2008). The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene, 408, 112–123. - PubMed

LinkOut - more resources