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Molecular phylogenetic tree of eight anemonefishes (Amphiprioninae) and Abudefduf vaigiensis (Pomacentrinae) from the same family Pomacentridae in suborder Labrodei. Chaetodon auripes (Percoidei: Chaetodontidae) was selected as an outgroup species. Congruent tree topology was inferred from partitioned Bayesian and Maximum Likelihood analyses using the concatenated nucleotide sequences of 13 protein-coding genes. The Bayesian posterior probability values (top) and boots trap values (bottom) were labeled at branch nodes. Branch length information from the Bayesian tree was shown. GenBank accession number of each species was listed on the right of the species name.
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Anemonefishes (Pomacentridae Amphiprioninae) are a group of 30 valid coral reef fish species with their phylogenetic relationships still under debate. The eight available mitogenomes of anemonefishes were used to reconstruct the molecular phylogenetic tree; six were obtained from this study (Amphiprion clarkii, A. frenatus, A. percula, A. periderai...
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... The gene content and arrangement of C. tritonis align with those of the previously reported mitogenomes from all species within the superfamily Tonnoidea (Choi and Hwang 2021). Unlike typical animal mitogenomes, it lacks a control region (Li et al. 2015). Charonia tritonis and C. lampas are grouped together within Charoniidae, forming a sister group to the other Tonnoidea families (Bursidae, Cassidae, Cymatiidae, and Tonnidae) (Supplementary Figure S2), which supports the proposed relationship as reported by previous studies (Cho et al. 2017;Strong et al. 2019;Choi and Hwang 2021). ...
The giant triton snail, Charonia tritonis (Linnaeus, 1758), crucial for coral reef ecosystems as a primary predator of the crown-of-thorns sea star, is experiencing a significant decline due to overfishing for its ornamental shell, underscoring the urgent need for conservation and deeper understanding of its role within marine biodiversity. This study presents the first complete mitogenome sequence of C. tritonis. Spanning 15,346 bp, the C. tritonis mitogenome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. Phylogenetic analysis of 88 Littorinimorpha mitogenomes confirms C. tritonis and C. lampas are grouped together within the family Charoniidae as a sister group to the remaining Tonnoidea families. This research not only enhances the taxonomic classification and conservation efforts for marine gastropods but also serves as a vital reference for future evolutionary and genetic studies within the Caenogastropoda.
... Clownfish have a high ornamental value and are an ideal material for studying the symbiotic behavior and co-evolution between clownfish and tropical sea anemones. To date, the limited number of studies of clownfish have mainly focused on traditional taxonomy, molecular phylogeny, and evolution (Santini and Polacco, 2006;Timm et al., 2008;James Cooper et al., 2009;Li et al., 2015;Hu et al., 2016;Ye et al., 2016;He et al., 2020). The current lack of species diversity remains a barrier in clownfish breeding. ...
... DNA was then extracted and purified for PCR amplifications. The mitochondrial cytochrome c oxidase subunit I (COI) gene is a candidate gene for studying the evolution of species, the primers (5′-TCAACCAACCACAAAGACATTGGCAC-3′ and 5′-TAGACTTCTGGGTGGCCAAAGAATCA-3′) were used to amplify this gene (Li et al., 2015;He et al., 2020). The PCR products were sequenced and the resulting nucleotide sequences were aligned with the COI gene sequences of Amphiprion akallopisos, A. frenatus, A. latifasciatus, A. ephippium, A. akindynos, A. clarkia, A. sebae, A. perideraion, A. bicinctus, A. barberi, A. chrysopterus, A. polymnus, A. sandaracinos, and A. percula, which were downloaded from National Center for Biotechnology Information (NCBI) using the MEGA v7 software (Kumar et al., 2016). ...
Since the release of the movie Finding Nemo, clownfish have been known and loved by many people. Clownfish have a very vivid skin color and extreme ornamental value. However, there are few species of clownfish, which greatly limits the breeding of new varieties. In this study, the Atmosphere and room temperature plasma (ARTP) method was used to treat clownfish-fertilized eggs and successfully screened out mutants that exhibited a skin color change from black to red in their offspring. To elucidate the molecular mechanism underlying this color mutation, more than 17,000 methylated peaks were obtained via m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-seq). These modification sites were mainly distributed around stop codons, and the number of corresponding genes exceeded 10,000. Further RNA sequencing (RNA-seq) of clownfish before and after the mutation was performed identified 883 genes that exhibited significant differences between the two samples, among which 152 interaction genes showed significant differences in the m6A methylated level and gene expression level. The results of a functional analysis showed that the phosphatidylinositol-3-kinase (PI3K)-serine/threoninekinase (Akt) pathway and its related signal pathways may play an important role in skin color change. In particular, genes such as mitogen activated protein kinase kinase 1 (MAP2K1), insulin―like growth factor―l (IGF1), and fibroblast growth factor 1 (FGF1) may play key roles in the accumulation of melanin in clownfish, and the homeobox-protein-encoding empty spiracles homeobox 2 (EMX2) and mesenchyme homeobox (MEOX2) genes may be important for determining the regions of accumulation of this skin pigment. Our results provide a new reference for the genetic breeding of clownfish and lay a foundation for further understanding the molecular mechanism underlying body color changes in clownfish.
... In anemonefishes, there has been no formal investigation of interspecific variation in their social behavior using phylogenetically controlled comparisons, even though their phylogenetic relationships have been well resolved (e.g., Elliott et al., 1999;Santini and Polacco, 2006;Litsios et al., 2012;Litsios and Salamin, 2014;Li et al., 2015;Rolland et al., 2018). However, there is some observed social variation between species that are ecologically similar, which indicates that Amphiprion species are good candidates for comparative studies. ...
Research on sociality in marine fishes is a vibrant field that is providing new insights into social evolution more generally. Here, we review the past two decades of research, identifying knowledge gaps and new directions. Two coral reef fishes, with social systems similar to other cooperative breeders, have emerged as models: the clown anemonefish Amphiprion percula and the emerald goby Paragobiodon xanthosoma. In these systems, non-breeders do not forgo their own reproduction to gain indirect genetic benefits. Rather, they do so because they stand to inherit the territory in the future and there are strong ecological and social constraints. The reasons why breeders tolerate non-breeders remain obscure, though it is plausibly a combination of weak kin selection, bet-hedging, and benefits mediated via mutualistic interactions with cnidarian hosts. The latter is particularly interesting, given the parallels with other social animals with mutualistic partners, such as acacia ants. Looking beyond the two model species, our attention is turning to species with more complex social organization, such as the damselfish Dascyllus aruanus. Here, variable group stability, conflict intensity, and reproductive skew provide opportunities to test theories of social evolution that have only been tested in a few taxa. New methods like social network analysis are enabling us to uncover more subtle effects of ecology on social interactions. More recently, comparative methods have yielded insights into the correlates of interspecific variation in sociality in the genera to which our model species belong. Phylogenetically controlled contrasts within the genus Gobiodon, have revealed the role of ecology, life history traits, and their interaction in sociality: smaller bodied species are more social than larger bodied species, which are only social on large corals. As climate change affects coral reefs, there is a pressing need to understand the many ways in which environmental disturbance influences these unique social systems. In sum, coral reef fishes have enabled us to test the robustness of current theories of social evolution in new taxa and environments, and they have generated new insights into social evolution that are applicable to a wider variety of taxa.
... ephippium, A. frenatus, A. mccullochi, A. melanopus, A. rubrocinctus) and a clarkii-complex (remaining species of the subgenus). Our study and many others (Koh et al., 2006;Santini and Polacco, 2006;Cooper et al., 2009;Cowman and Bellwood, 2011;Litsios et al., 2012aLitsios et al., , 2012bFrédérich et al., 2013;Rabosky et al., 2013Rabosky et al., , 2018O'Donnell, 2014;Dhaneesh et al., 2015;Li et al., 2015;DiBattista et al., 2016;Mirande, 2016;Thongtam na Ayudhaya et al., 2017Gaboriau et al., 2018;Rolland et al., 2018;Delrieu-Trottin et al., 2019;Nguyen et al., 2020) have provided ample evidence for the monophyly of Actinicola, which encompasses the two clownfish species, A. ocellaris and A. percula. As a subgenus of Amphiprion, Premnas is sister to Actinicola. ...
... Other species with one or fewer bars are also found outside of this clade (e.g., A. nigripes, A. omanensis, and A. perideraion). The subgeneric names have seen sporadic use (e.g., Elliott et al., 1999;Tang, 2001;Santini and Polacco, 2006;Steinke et al., 2009;Dhaneesh et al., 2015;Li et al., 2015;Hu et al., 2016;Nguyen et al., 2020), and any future recognition would require revision of their limits. ...
... This is in agreement with Elliott et al. (1999), who first suggested the specialist ancestor of anemonefish in their study. The paraphyly of the Amphiprion genus, and nonmonophyletic topologies of the subgenera Amphipiron, Phalerebus and Paramphiprion were also indicated in previous studies (Jang-Liaw et al. 2002;Litsios et al. 2014;Li et al. 2015). Premnas biaculeatus was placed within the Amphiprion genus in our phylogeny, as previously proposed (Elliott et al. 1999;Santini and Polacco 2006;Litsios et al. 2012). ...
The association between anemonefish and anemone is a classical example of mutualism in coral reefs. Although mutualism is probably the key innovation that triggered the adaptive radiation of anemonefish into a wide range of habitats, the coevolutionary history between the groups has not been thoroughly tested in a phylogenetic framework. We examined the evolutionary history of the association via distance-based (Parafit and PACo) and event-based methods (Core-PA, Jane). Mitochondrial DNA sequences (COI mtDNA, Cytb, 16S rDNA and 12S rDNA) were used to reconstruct the phylogenies of tropical Amphiprion species and their host anemones by using maximum likelihood with best-fit models selected. Neither distance-based analyses nor event-based analyses revealed global significant congruence between the phylogenies of the hosts and the symbionts, and thus no evidence for coevolution between anemone-anemonefish. However, at the individual pair level, the fish showed some dependence on anemone hosts. Even though living in close association and benefiting from each other, the change of genetic composition of one species (anemonefish) does not always evolve in response to changes in the other (anemones). These findings expand our understanding of the pattern and the role of evolutionary events to allow a better prediction of the future of the anemonefish-anemone relationship.
... One specimen of J. taiwanensis (FJDS20160317) was collected by hook-and-line in the coastal water of Dongshan County, Fujian Province, China. The protocol and data analysis methods were according to Li et al. (2015). The complete mitochondrial genome of J. taiwanensis is 18,451 bp in length (GenBank accession number: MG917694) with the typical gene order and transcriptional direction in vertebrates and with gene rearrangement feature. ...
In this study, the complete mitogenome of a new species, Johnius taiwanensis (Chao et al. 2019) was obtained. Its mitogenome is 18,451 bp in length, consisting of 37 genes with the typical gene order and direction of transcription in vertebrates. Gene rearrangement was found in J. taiwanensis. The overall nucleotide composition is: 24.2% A; 18.0% C; 21.1% G, and 36.7% T. Sizes of the 22 tRNA genes range from 66 to 75 bp. Two start codons (ATG and GTG) and three stop codons (TAG, AGA and TAA/TA/T) were detected in 13 protein-coding genes. In the Bayesian tree based on the complete mitogenomes of 26 species (including J. taiwanensis) from the family Sciaenidae, all nodes were strongly supported. The result shows that J. taiwanensis was placed as sister to the Trewavas croaker J. trewavasae of the same genus. The mechanism of gene rearrangement in the genus Johnius merits further investigation.
... The specimen of R. glesne (Voucher: SY2015102354) was collected on the fish pier from Sanya, Hainan Province. The experimental protocol of DNA extraction and data processing methods of raw data was according to the method described by Li et al. (2015). The complete mitogenome had a doublestranded DNA molecule with the length of 16,536 bp (GenBank accession no.MK209627), containing 37 genes (13 protein-coding genes, 2 rRNA genes, 22 tRNA genes) and one control region with a typical mitogenomic organization and gene orders in line with other vertebrates. ...
The mitochondrial genome of Regalecus glesne was firstly elucidated and analyzed in this study. It had a double-stranded DNA molecule with the length of 16,536 bp and was made up 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one control region. Furthermore, the phylogenetic result demonstrated that R. glesne clustered with Trachipterus trachypterus and Zu cristatus. The complete mitochondrial genome provided in this work would be helpful for the genetic elucidation of the evolution of Lampriformes and other orders.
... The tissue of L. fornasini (voucher No. OKA2016061113) was collected from Okinawa Island, Japan. The experimental protocol and data analysis methods followed Li et al. (2015). Excluding L. fornasini, 20 species of Tetraodontiformes were selected to conduct the phylogenetic tree. ...
The complete mitochondrial genome of the box-like thornback cowfish (Lactoria fornasini) was first determined in this study. It was a circular molecule of ∼1.6 kb, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region. Of the 37 genes, 28 were encoded by the heavy strand, while the rest were encoded by the light strand. The genome composition with A + T bias (56.22%) and gene arrangement were almost identical with those observed in most vertebrates. The 22 tRNA genes ranged from 66 bp (tRNA-Cys) to 75 bp (tRNA-Lys). The phylogenetic result showed that L. fornasini was clustered with L. diaphana.
... Most are distinguished by their color patterns; however, several species show variable morphs (Allen 1975). Recent molecular analyses reported color patterns as not always sufficient indicators of species diversity (Li et al. 2015;Thongtam na Ayudhaya et al. 2017). Genetic diversity studies of more molecular markers will provide important information for systematic conservation anemonefish management. ...
... All PCR products were sequenced by DNA sequencing service, First Base Laboratories Sdn Bhd (Selangor, Malaysia), with annotation performed following Srikulnath et al. (2012) and Prakhongcheep et al. (2018). Mitogenome sequence size of 10 anemonefishes (16,762-16,980 bp) was similar to previous reports (Mabuchi et al. 2007;Li et al. 2015;Hu et al. 2016;Tao et al. 2016). All mitogenomes comprised 37 genes and a control region (CR). ...
... Gene organization patterns were identical to teleosts (Miya et al. 2013). GAT deletion was found in ND5 of A. percula and A. ocellaris differed from previous reports with CCT deletion (Li et al. 2015), suggesting the possibility of intra-specific variation. Nucleotide diversity among anemonefish mitogenomes was 8.36 ± 0.27%, with sequence divergence between Amphiprion and Premnas at 10.98%. ...
Anemonefish are widely distributed in tropical areas with phenotypic color variation often observed in the same species. Complete mitochondrial genomes (mitogenomes) of 10 anemonefishes belonging to Amphiprion and Premnas were determined to support taxonomic status. Average mitogenome sequence was 16,838 ± 19.69 bp, containing 37 genes with identical gene order to most teleost mitogenomes. The percula complex comprised A. percula and A. ocellaris and was phylogenetically clustered with P. biaculeatus. Color morphs of A. ocellaris and P. biaculeatus were identified, suggesting large phenotypic variation at species level. Results will facilitate further genetic studies of mitochondrial variation and species diversity in anemonefish.
... The orange clownfish is one of 30 species of anemonefishes belonging to the subfamily Amphiprioninae within the family Pomacentridae (damselfishes). The two clownfishes, A. percula (orange clownfish or clown anemonefish) and A. ocellaris (false clownfish or western clown anemonefish), form a separate clade, alongside Premnas biaculeatus, within the Amphiprioninae (Li, Chen, Kang, & Liu, 2015;Litsios, Pearman, Lanterbecq, Tolou, & Salamin, 2014). The two species of clownfish are easily distinguished from other anemonefishes by their bright orange body coloration and three vertical white bars. ...
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome‐scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single‐molecule real‐time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi‐C‐based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein‐coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
