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. 2025 Sep 8;10(10):932–936. doi: 10.1080/23802359.2025.2554415

The mitochondrial genome of an invasive hydromedusa: Cladonema digitatum Fang et al., 2022 (Cnidaria: Hydrozoa)

Yuxiang Huang a,b, Jiaxin Tian b,c, Shuo Zheng a,b, Ping Zheng c, Jianming Chen b, Konglin Zhou b,✉, Weicheng Wang a,✉
PMCID: PMC12418794  PMID: 40933617

Abstract

This study presents the first mitochondrial genome (16,342 bp) of the invasive species Cladonema digitatum Fang et al., 2022, revealing a conserved Capitata-like gene arrangement, comprising 13 protein-coding genes, two rRNA genes, and two tRNA genes, along with a duplicated pseudo-cox1 fragment. Phylogenetic analysis robustly supported C. digitatum and Cladonema multiramosum as reciprocally monophyletic mitogenome lineages, forming a robust clade sister to Cladonema pacificum. This topology supports the morphological dichotomy between the Cladonema radiatum-like lineage (filiform tentacles, gastric pouches) and C. pacificum-like species. These findings contribute a critical genomic resource for advancing the understanding of medusozoan phylogeny.

Keywords: Mitogenome map, phylogenetic analysis, pseudo-cox1, gene arrangement, Cladonema

Introduction

Hydromedusae are ecologically vital in marine ecosystems and evolutionarily significant in Cnidaria (Graham et al. 2014; Kayal et al. 2018). Among them, Cladonema species have been esteemed as valuable model organisms for multidisciplinary researches spanning ecology, developmental biology, regeneration, neuroscience, and evolutionary genomics (Takeda et al. 2018; Fujita et al. 2019, 2021; Hou et al. 2021; Masuda-Ozawa et al. 2022; Fujita et al. 2023, Lin et al. 2024). Despite their ecological importance, Cladonema species exhibit invasive tendencies in both natural and artificial environments, threatening cultivated species such as Oryzias melastigma (Miglietta et al. 2008; Cedeño-Posso 2014; Fang, Lin et al. 2022; Zhou et al. 2022; Lin et al. 2024). Persistent taxonomic ambiguities arise from morphological plasticity and convergence among Cladonema species, resulting in synonymy issues and potential oversight of cryptic diversity (Schuchert 2006; Ahuatzin-Hernández et al. 2022). DNA barcoding using 16S and COI markers has improved Cladonema classification, but discordances persist between genetic similarity and morphological divergence (Bucklin et al. 2010; Fang, Lin, et al. 2022). Phylogenetic reconstructions also revealed topological conflicts: Cladonema was resolved as a monophyletic group in multi-locus analyses (Maggioni et al. 2024), but exhibited polyphyly exclusively in COI-based trees (Fang, Lin, et al. 2022). Mitochondrial genomes, characterized by accelerated evolutionary rates relative to nuclear DNA, offer enhanced resolution for resolving lower taxonomic relationships and clarifying medusozoan phylogeny (Kayal et al. 2015; Chan et al. 2021; Ling et al. 2023). Despite this potential, only two mitochondrial genomes (Cladonema pacificum and Cladonema multiramosum) have been documented within the genus and family Cladonematidae (Kayal et al. 2015; Fang, Zhou, et al. 2022). Here, we present the mitochondrial genome of Cladonema digitatum Fang, Lin, et al. (2022), providing a critical genomic resource to advance phylogenetic reconstruction.

Materials and methods

Cladonema digitatum has invaded O. melastigma aquaculture systems, yet its ecological spread in natural habitats remains unassessed (Fang, Lin, et al. 2022). C. digitatum specimens (Figure 1) were collected in 2021 from an O. melastigma aquarium and maintained alive in the Institute of Oceanography, Minjiang University, Fuzhou, China. The voucher specimens were deposited in Marine Biodiversity Laboratory of Minjiang University (voucher numbers: MJU-HYD-6-9; contact: Konglin Zhou, zhoukl@mju.edu.cn). The DNA was extracted from a pool of five medusae, fasted for 72h, using a TIANnamp Marine Animals DNA Kit (TIANGEN, Beijing, China). After DNA quality assessment, DNA library was constructed with a 350 bp insert size and sequenced on the Illumina NovaSeq 6000 platform (paired-end 150 bp reads, 10 Gb in total) at Novogene Co., Ltd. (Beijing, China). Raw reads were processed with Trimmomatic v0.38 (Bolger et al. 2014) for adapter trimming and quality filtering to generate clean reads. The mitochondrial genome was de novo assembled using both Getorganelle v1.7.7.1 (Jin et al. 2020) and NOVOPlasty v4.3.1 (Dierckxsens et al. 2017) with clean reads, using the mitochondrial genome of C. pacificum (KT809323) as reference sequence for baiting. The read coverage depth was calculated using samtools v1.7 (Li et al. 2009), and the average depth was 3509 ± 723 (mean ± SD; visualized in R v4.3.1 in Supplementary Figure S1). Preliminary annotation was performed using MITOS2 (Al Arab et al. 2017; Donath et al. 2019). Annotation validation included ORF Finder and BLASTX on NCBI for protein-coding genes (PCGs), Barrnap v0.9 for rRNAs (Seemann 2013), tRNAscan-SE 2.0 for tRNAs (Lowe and Chan 2016), and Inverted Repeats Finder v3.08 (Warburton et al. 2004) for inverted repeat sequences (IRSs). The mitogenome map was generated using the OGDRAW (Greiner et al. 2019).

Figure 1.

Figure 1.

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The image of Cladonema digitatum deposited in Minjiang University, photographed by Xinyu Fang. (A) Mature medusae; (B) Polyp with a medusa bud.

Twelve hydrozoan mitogenomes, including ten Capitata species and two Aplanulata species (Hydra sinensis and Hydra oligactis, used as outgroups), were obtained from NCBI GenBank. Phylogenetic analysis was conducted using PhyloSuite v1.2.3 (Zhang et al. 2020). The 13 PCGs were aligned with MAFFT v7.505 (Katoh and Standley 2013), trimmed using Gblocks (Talavera and Castresana 2007), and concatenated. The optimal substitution model was selected using ModelFinder v2.2.0 (Kalyaanamoorthy et al. 2017). Finally, a maximum likelihood (ML) phylogenetic tree was constructed with IQ-TREE (Nguyen et al. 2015) under the GTR+F + I + G4 model and a Bayesian (BI) phylogenetic tree was reconstructed using MrBayes (Ronquist et al. 2012) under the GTR+I + G model, with 1000 bootstrap replicates. The tree was visualized using iTOL v7 (Letunic and Bork 2024).

Results

The linear mitochondrial genome of C. digitatum (16,342 bp) exhibited characteristic hydrozoan genomic architecture with highs AT-rich composition (A: 28.289%; T: 40.558%; C: 15.157%; G: 15.996%). It encoded 13 PCGs (cox1-3, atp6/8, nad1-6, nad4l, cob), two rRNAs (rrnS, rrnL), and two tRNAs (trnW, trnM), but lacked IRSs (Figure 2). All genes were on the plus strand, except rrnL and a very short duplicated 3′ end of cox1 (94 bp) on the minus strand. The mitochondrial genome exhibited limited structural complexity, with both overlapping regions (sparsely distributed and typically ≤ 10 bp in length) and intergenic regions shown in Figure 2. All 13 PCGs used ATG as the start codon, while termination codons revealed distinct patterns: nad5, nad6 and cox1 utilized TAG as stop codons, and the remaining ten used TAA.

Figure 2.

Figure 2.

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Mitochondrial genome map of Cladonema digitatum. Genes transcribed from the heavy and light strands are shown above and below the chain, respectively.

Phylogenetic analysis with full nodal support resolved C. digitatum and C. multiramosum as reciprocally monophyletic mitogenome lineages, forming a robust clade sister to C. pacificum (Figure 3).

Figure 3.

Figure 3.

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Phylogenetic relationships of Cladonema digitatum within Capitata. The maximum-likelihood and Bayesian trees were reconstructed from 13 mitochondrial PCGs, with nodal supports shown as bootstrap values (≥70%, 1000 replicates; left) and posterior probabilities (≥0.8; right), with two Aplanulata species (Hydra sinensis and Hydra oligactis) as outgroups. Red bold indicates the focal species (C. digitatum PV035242). The following sequences were used: Cladonema pacificum KT809323 (Kayal et al. 2015), Cladonema multiramosum MZ747707 (Fang, Zhou, et al. 2022), Cladonema digitatum PV035242 (this study), Millepora sp. EK-2011 JN700943 (Kayal et al. 2012), Millepora alcicornis OZ218849 (unpublished), Millepora complanata OZ210633 (unpublished), Millepora dichotoma OZ218617 (unpublished), Pennaria disticha JN700950 (Kayal et al. 2012), Spirocodon saltatrix MT150265 (Seo et al. 2020), Sarsia tubulosa KT809333 (Kayal et al. 2015), H. sinensis (Pan et al. 2014), and H. oligactis (Kayal and Lavrov 2008). The red bold font highlights the focal species of this study.

Discussion and conclusion

Generally, medusozoan mitogenomes show three mtDNA gene orders patterns (Feng et al. 2023). The gene arrangement of C. digitatum (Figure 2; pseudo cox1-rrnL-cox2-trnW-atp8-atp6-cox3-trnM-nad2-nad5- rrnS -nad6-nad3-nad4l-nad1-nad4-cob-cox1) aligned with conserved syntenic blocks in Capitata mitogenomes (Ahuja et al. 2024). In Capitata, the pseudo cox1 has been found in several species including C. pacificum (KT809323), C. multiramosum (MZ747707), Millepora dichotoma (OZ218617) and Spirocodon saltatrix (MT150265), but not found in other species with only partial mitogenomes, such as Millepora sp. (JN700943), Millepora complanata (OZ210633), Millepora alcicornis (OZ218849), Pennaria disticha (JN700950), and Sarsia tubulosa (KT809333). This replication and inversion of pseudo cox1 was common in Siphonophorae, Anthoathecata, and Leptothecata (Kayal et al. 2015; Ling et al. 2023), and it may not have any function, indeed.

In this study, the phylogenetic results corroborated prior studies (Ling et al. 2023), and supported the C. radiatum-like versus C. pacificum-like dichotomy, which was strongly validated by prior multi-locus studies combining morphological and molecular analyses based on 16S and COI sequences (Fang, Lin, et al. 2022; Zhou et al. 2022). Specifically, C. digitatum and C. multiramosum exhibited key morphological synapomorphies of the C. radiatum lineage, including filiform tentacles in hydroids and gastric pouches in medusae (Fang, Lin, et al. 2022; Zhou et al. 2022). Given the polyphyletic outcomes observed within the family Cladonematidae using 16S and COI markers (Fang, Lin, et al. 2022), further mitogenomic data from additional Cladonematidae species are required to elucidate the phylogenetic relationships within the genus Cladonema and the broader family Cladonematidae.

Supplementary Material

Supplementary Figure S1.docx
TMDN_A_2554415_SM8951.docx (229.8KB, docx)

Acknowledgments

Xinyu Fang is Jianming Chen’s student, and we appreciate her help with taking photos of Cladonema digitatum in our lab.

Funding Statement

This work was supported by Open Project of Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University (Grant No. CSUMBL2023-4), the National Natural Science Foundation of China (No. 41806181), the Natural Science Foundation of Fujian Province of China (No. 2021J011042), and The Talent introduction pre-research project of Minjiang University (No. MJY20017).

Ethical approval

The material of this paper does not involve ethical conflicts. Cladonema digitatum is neither endangred on the CITES catalog nor collected from a natural reserve. Cladonema digitatum used in this study was approved by the Ethical Committee of Minjiang University.

Author contributions

All the authors approved the submitted version of this manuscript and agreed to be accountable for all aspects of the work. CRediT: Yuxiang Huang: Data curation, Formal analysis, Writing – original draft; Jiaxin Tian: Formal analysis, Visualization, Writing – original draft; Shuo Zheng: Investigation, Writing – original draft; Ping Zheng: Formal analysis, Writing – review & editing; Jianming Chen: Conceptualization, Resources, Writing – review & editing; Konglin Zhou: Funding acquisition, Project administration, Supervision, Validation, Writing – review & editing; Weicheng Wang: Conceptualization, Supervision, Writing – review & editing.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession No. PV035242. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1219306, SRR32240099, and SAMN46553284 respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Figure S1.docx
TMDN_A_2554415_SM8951.docx (229.8KB, docx)

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession No. PV035242. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1219306, SRR32240099, and SAMN46553284 respectively.

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