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. 2022 Apr 18:10:e13275.
doi: 10.7717/peerj.13275. eCollection 2022.

Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera)

Zwannda Nethavhani  1 , Rieze Straeuli  1 , Kayleigh Hiscock  1 , Ruan Veldtman  2   3 , Andrew Morton  4 , Rolf G Oberprieler  5 , Barbara van Asch  1
Affiliations

Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera)

Zwannda Nethavhani et al. PeerJ. .

Abstract

African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies.

Keywords: Attacini; Bunaeini; Edible insects; Eochroini; Micragonini; Mitogenome; Phylogenetics; Saturniidae; Southern Africa.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Representative specimens of 12 African Saturniidae species.
Larva and adult specimens used in this study for new mitogenomic sequencing and phylogenetic analyses or collected from the same area. (A) Nudaurelia wahlbergii (Boisduval, 1847), (B) Nudaurelia cytherea (Fabricius, 1775), (C) Bunaea alcinoe (Stroll, 1780), (D) Gonimbrasia tyrrhea (Cramer, 1776), (E) Heniocha apollonia (Cramer, 1779), (F) Heniocha dyops (Maassen, 1872), (G) Vegetia ducalis (Jordan, 1922), (H) Vegetia grimmia (Geyer, 1832), (C) Holocerina smilax (Westwood, 1849), (D) Ludia delegorguei (Boisduval, 1847), (J) Eochroa trimenii (C. & R. Felder, 1874), and (L) Epiphora bauhiniae (Guérin-Méneville, 1832).
Figure 2
Figure 2. Mitochondrial gene organization.
Linear map of the complete mitochondrial genomes of (A) African Saturniidae and (B) hypothetical ancestral of the non-Ditrysian lineage Hepialoidea of Lepidoptera.
Figure 3
Figure 3. Structure of tRNA-Ser in 12 African Saturniidae species.
Predicted structure of tRNASer1 in the complete mitochondrial genomes of 12 new and two previously sequenced African Saturniidae species. Inferred canonical Watson-Crick bonds are represented by lines, and non-canonical bonds are represented by dots.
Figure 4
Figure 4. Nucleotide composition of Saturniidae mitogenomes.
Nucleotide composition in 14 complete mitochondrial genomes of African Saturniidae (Lepidoptera). (A) AT% content, (B) GC% content, (C) AT-skew, and (D) GC-skew for individual genes, total protein-coding genes (PCG), individual rRNAs and complete mitogenomes.
Figure 5
Figure 5. Usage of start and stop codons in Saturniidae mitogenomes.
Usage of start and stop codons of 13 protein-coding genes in 14 mitogenomes of African Saturniidae species.
Figure 6
Figure 6. Codon frequencies in Saturniidae mitogenomes.
(A) Mean codon frequencies and (B) standard deviation in the mitochondrial protein-coding genes of 14 African Saturniidae. Vertical axis: Protein-coding genes; Horizontal axis: Single-letter amino acid codons.
Figure 7
Figure 7. Relative synonymous codon usage in Saturniidae mitogenomes.
Average relative synonymous codon (RSCU) usage in the mitochondrial protein-coding genes of 14 African Saturniidae species. Vertical axis: RSCU; Horizontal axis: Single-letter amino acid codons. Black dots represent outliers that differ significantly from other observations.
Figure 8
Figure 8. Ka, Ks and Ka/Ks rates in Saturniidae mitogenomes.
Rates of non-synonymous and synonymous substitutions in the 13 mitochondrial protein-coding genes of 14 African Saturniidae species. Vertical axis: protein-coding genes; horizontal axis: Ka - number of nonsynonymous substitutions per non-synonymous site; Ks -number of synonymous substitutions per synonymous site.
Figure 9
Figure 9. ML and MrBayes trees of Saturniidae species.
Maximum likelihood and MrBayes trees of the mitochondrial phylogeny of the family Saturniidae (Lepidoptera) based on 13 protein-coding genes (all codon positions). (A) MrBayes tree under the GTR+G+I model. Nodal support is given as Bayesian posterior probability. (B) Maximum-likelihood tree. Nodal support is shown as ultrafast bootstrap support (UFBoot)/approximate likelihood ratio test (SH-aLRT).
Figure 10
Figure 10. PhyloBayes tree of Saturniidae species.
PhyloBayes tree of the mitochondrial phylogeny of the family Saturniidae (Lepidoptera) based on 13 protein-coding genes (all codon positions) under the CAT+GTR mixed model. Nodal support is given as Bayesian posterior probability.
See this image and copyright information in PMC

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Further Reading

    1. Chen MM, Li Y, Chen M, Wang H, Li Q, Xia RX, Zeng CY, Li YP, Liu YQ, Qin L. Complete mitochondrial genome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae) and the phylogenetic relationship of Saturniidae species. Gene. 2014;545:95–101. doi: 10.1016/j.gene.2014.05.002. - DOI - PubMed
    1. Hong MY, Lee EM, Jo YH, Park HC, Kim SR, Hwang JS, Jin BR, Kang PD, Kim KG, Han YS, Kim I. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene. 2008;413:49–57. doi: 10.1016/j.gene.2008.01.019. - DOI - PubMed
    1. Liu Y, Pan MLiY, Dai F, Zhu X, Lu C, Xiang Z. The complete mitochondrial genome of the Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae) Acta Biochimica et Biophysica Sinica. 2008;40:693–703. doi: 10.111/j.1745-7270.2008.00449.x. - DOI - PubMed
    1. Liu QN, Zhu BJ, Dai LS, Wei GQ, Liu CL. The complete mitochondrial genome of the wild silkworm moth, Actias selene. Gene. 2012;505:291–299. doi: 10.1016/j.gene.2012.06.003. - DOI - PubMed
    1. Park JS, Kim MJ, Kim I. The complete mitochondrial genome of the moon moth, Actias aliena (Lepidoptera: Saturniidae) Mitochondrial DNA Part A. 2016;27:149–150. doi: 10.3109/19401736.2013.878918. - DOI - PubMed

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