.2023 Oct 18;26(11):108252.

doi: 10.1016/j.isci.2023.108252. eCollection 2023 Nov 17.

Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes

Min Kang Ling¹, Nicholas Wei Liang Yap^{2 3}, Iffah Binte Iesa⁴, Zhi Ting Yip¹, Danwei Huang^{1 2 4}, Zheng Bin Randolph Quek^{1 5}

Affiliations

¹ Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
² Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore.
³ St. John's Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore.
⁴ Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore.
⁵ Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.

PMID:37965150
PMCID: PMC10641506
DOI: 10.1016/j.isci.2023.108252

Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes

Min Kang Ling et al. iScience.2023.

.2023 Oct 18;26(11):108252.

doi: 10.1016/j.isci.2023.108252. eCollection 2023 Nov 17.

Authors

Min Kang Ling¹, Nicholas Wei Liang Yap^{2 3}, Iffah Binte Iesa⁴, Zhi Ting Yip¹, Danwei Huang^{1 2 4}, Zheng Bin Randolph Quek^{1 5}

Affiliations

¹ Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
² Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore.
³ St. John's Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore.
⁴ Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore.
⁵ Yale-NUS College, National University of Singapore, Singapore 138527, Singapore.

PMID:37965150
PMCID: PMC10641506
DOI: 10.1016/j.isci.2023.108252

Abstract

Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.

Keywords: genomics; phylogeny.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Figure 1**
Hypotheses of cnidarian phylogenetic relationships based on previous mitogenomic analyses (A–C) (A) Zou et al.; (B) Kayal et al.; and (C) Feng et al.

**Figure 2**
Phylogenetic relationships among Cnidaria mitogenomes based on maximum likelihood (ML) and Bayesian (BI) analyses (A and B) (A) Ulmaridae; (B) [Mastigiidae +*Acromitus*] clade. Support values correspond to the bootstrap values from the ML phylogeny (BS ≥ 50%) and posterior probabilities from the BI analysis (pp ≥ 0.8). For nodes with differences in topology, only the bootstrap values (BS ≥ 50%) were provided. Posterior probabilities for these nodes were denoted with a dash (−). GenBank ascension numbers of mitogenomes are provided in parentheses. Bolded specimens indicate newly assembled mitogenomes from the current study. The degree (°) symbol denotes available mitogenome recorded as circular on GenBank.

**Figure 3**
Comparison of gene order of Medusozoa mitochondrial genes with reference to the Maximum Likelihood (ML) phylogeny, using complete cnidarian mitogenomes For mitogenomes with multiple chromosomes, vertical lines denote breaks between each chromosomal fragment. Complete mitochondrial genes are indicated in color, while pseudogenes (as indicated on GenBank) are colored but outlined with dotted lines. Missing genes are represented by uncolored boxes outlined with dotted lines. (A–I) Mitochondrial rearrangements indicated using black arrows: (A) Ancestral medusozoan gene order (AMGO); (B) fragmentation of mitochondrial genome, loss oftrnW; (C) loss oftrnW,*rnl*,*polB*, andorf314, (D) inverse transposition ofrnl and loss ofpolB andorf314; (E) loss of gene pairpolB-*orf314*, and duplication, transposition, and inversion ofcox1; (F) inversion ofrnl and transposition oftrnW; (G) transposition oftrnM; (H) fragmentation and duplication ofcox1; (I) inversion and transposition ofrnl, as well as transposition ofrns,*cox1*,*atp6*, andnad1. Asterisks (∗) denote the phylogenetic positions of specimens assembled in current study: Scyphozoa –*Acromitus* sp.,*Cassiopea* sp.,*Phyllorhiza punctata*; Hydrozoa –*Zygocanna* sp.,*Aequorea* sp.; Cubozoa –*Morbakka* sp.

**Figure 4**
Results from the TreeRex analysis of the RAxML medusozoa phylogeny Where applicable, inferred mitochondrial genome rearrangements are listed at the corresponding nodes. Gene order rearrangements are as follows:I – inversion;T - transposition;iT – inverse transposition;*TDRL* – tandem duplication random loss. Genes undergoing rearrangements are indicated in parentheses. Labels at nodes denote the inferred gene order for the common ancestor as listed in the ML TreeRex analysis output (Data S1).

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References

1. Park E., Hwang D.-S., Lee J.-S., Song J.-I., Seo T.-K., Won Y.-J. Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Mol. Phylogenet. Evol. 2012;62:329–345. - PubMed
1. Quattrini A.M., Rodríguez E., Faircloth B.C., Cowman P.F., Brugler M.R., Farfan G.A., Hellberg M.E., Kitahara M.V., Morrison C.L., Paz-García D.A., et al. Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time. Nat. Ecol. Evol. 2020;4:1531–1538. - PubMed
1. Kayal E., Bentlage B., Sabrina Pankey M., Ohdera A.H., Medina M., Plachetzki D.C., Collins A.G., Ryan J.F. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evol. Biol. 2018;18:68.
1. McFadden C.S., Ofwegen L.P., Quattrini A.M. Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics. BSSB. 2022;1:1–79.
1. Novosolov M., Yahalomi D., Chang E.S., Fiala I., Cartwright P., Huchon D. The phylogenetic position of the enigmatic, Polypodium hydriforme (Cnidaria, Polypodiozoa): Insights from mitochondrial genomes. Genome Biol. Evol. 2022;14 - PMC - PubMed

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Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes

Affiliations

Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

LinkOut - more resources

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