The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia)

The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia) | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia) View ORCID Profile Yuki Yoshioka , Megumi Kanai , Tatsuki Koido , Noriyuki Satoh , Tomofumi Nagata doi: https://doi.org/10.1101/2025.10.14.682458 Yuki Yoshioka 1 Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University , Onna, Okinawa 904-0495, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yuki Yoshioka For correspondence: y.yoshioka{at}oist.jp Megumi Kanai 2 Incorporated Foundation Okinawa Environment Science Center , Urasoe, Okinawa 901-2111, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tatsuki Koido 3 Kuroshio Biological Research Foundation , Otsuki, Kochi 788-0333, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Noriyuki Satoh 1 Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University , Onna, Okinawa 904-0495, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tomofumi Nagata 3 Kuroshio Biological Research Foundation , Otsuki, Kochi 788-0333, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract In this study, we sequenced the complete mitochondrial genomes (mitogenome) of Litophyton sp. and Stereonephthya sp. (family Nephtheidae), collected in Okinawa, Japan. The complete mitogenomes of Litophyton sp. and Stereonephthya sp. were 19,130 bp and 18,912 bp in length, respectively. They contained 17 genes (14 protein-coding genes, two rRNA genes, and one tRNA gene) and exhibited gene order pattern “A”, which is the most common arrangement among octocorals. Molecular phylogenetic analysis indicated that Litophyton sp. And Stereonephthya sp. are clustered with other species belonging to family Nephtheidae, consistent with the previous research using partial mitochondrial genes. Our study provides additional mitochondrial genomic resources that contributes to comparative studies of octocoral mitogenomes. Introduction The anthozoan class Octocorallia Haeckel, 1866 comprises more than 3,500 described species ( Williams and Cairns, 2019 ) inhabiting a wide range of marine environments, from shallow coral reefs to the deep sea ( Cairns, 2007 ; Dinesen, 1983 ). The Octocorallia is phylogenetically divided into two clades, the orders Malacalcyonacea and Scleralcyonacea ( McFadden et al., 2022 ). The genetic feature unique to octocorals is the presence of the mutS gene in their mitogenome ( mt - mutS ), a homolog of the epsilonproteobacterial mismatch repair gene mutS ( Bilewitch and Degnan, 2011 ; McFadden et al., 2010 ; Pont-Kingdon et al., 1995 ). The genera Litophyton Forskål, 1775 and Stereonephthya Kükenthal, 1905 belong to family Nephtheidae Gray, 1862. Their habitat ranges from shallow to moderately deep waters of tropical Indo-Pacific ( McFadden et al., 2022 ). This family is widely used for chemical investigation. Since 1985, over 344 compounds, including steroids, have been isolated ( Hu et al., 2011 ; Mahmoud et al., 2025 ; Yu et al., 2024 ). However, species identification of octocorals based solely on morphology remains challenging, often even to genus. Therefore, genomic resources based on an integrated taxonomic approach are indispensable for accurate taxonomic resolution. To date, complete mitogenomes for these two genera have not been reported. We here report the complete mitogenomes of Litophyton sp. and Stereonephthya sp., and their phylogenetic positions based on mitogenomes. Materials and Methods We collected a colony of Litophyton sp. and Stereonephthya sp. in the reef slope (at approximately 13 m in depth) around Sunabe (latitude: 26.327401 and longitude: 127.743660 for Litophyton sp.; latitude: 26.32216 and longitude: 127.74468 for Stereonephthya sp.), Okinawa-jima, Japan in June 2024 ( Figure 1 ). Specimens were deposited at Incorporated Foundation Okinawa Environment Science Center, Okinawa, Japan ( https://www.okikanka.or.jp/ , contact parson: Megumi Kanai, email: m.kanai{at}okikanka.or.jp ) under the voucher number “Soft_Coral_98” and “Soft_Coral_106”. Samples were fixed with 99.5% ethanol immediately after collection. Species was identified through scanning electron microscopy observation of sclerites (JCM-7000 NeoScope™, JEOL Ltd.). Both specimens were bush-like colonies and monomorphic polyps that contract but are non-retractile. In ‘Soft_Coral_98’, the polyps form in catkins along the branches. In contrast, ‘Soft_Coral_106’ has polyps arising singly or in small groups from over the polyparium. In the polyps, “Soft_Coral_98” lacks distinct supporting bundles and points, whereas ‘Soft_Coral_106’ has conspicuous supporting bundles and points. The sclerites of both specimens are predominantly spindle-shaped. Based on these characteristics, the specimens ‘Soft_Coral_98’ and ‘Soft_Coral_106’ were identified as Nephthya sp. and Stereonephthya sp., respectively, by Tatsuki Koido. Genomic DNA was extracted from the capitulum using a Maxwell RSC Blood DNA Kit (Promega). Sequence libraries were constructed with NEBNext Ultra II FS DNA PCR-free Library Prep Kit for Illumina according to the manufacturer’s protocol and were sequenced on a NovaSeq X, with 150-bp paired-end reads. Illumina sequence adaptors and low-quality sequences (quality cutoff=20) were trimmed with CUTADAPT v4.3 ( Martin, 2011 ). Cleaned reads were assembled with GetOrganelle v1.7.7.0 ( Jin et al., 2020 ). The sequencing depth was calculated with BamDeal v0.27 ( https://github.com/BGI-shenzhen/BamDeal ). Mitochondrial gene annotation was performed with MITOS2 ( Bernt et al., 2013 ) and subsequently refined through manual curation. Complete mitogenomes with gene annotation were visualized with OrganelleGenomeDRAW ( Greiner et al. 2019 ). We performed molecular phylogenetic analysis following Yoshioka et al. (2025) . Acrophytum claviger NC_061990.1 belonging to family Acrophytidae was used for outgroups. Download figure Open in new tab Figure 1. Photographs of Litophyton sp. (credit: Tatsuki Koido) and Stereonephthya sp. (credit: Tomofumi Nagata). Both genera shape bush-like colonies and monomorphic polyps that contract but are non-retractile. Stereonephthya sp. has polyps arising singly or in small groups from over the polyparium, and the polyps of this genus have conspicuous supporting bundles and points. In contrast, the polyps of Nephthya sp. form in catkins along the branches and lack distinct supporting bundles and points. The sclerites of both genera are predominantly spindle-shaped. Results We successfully obtained the complete mitogenomes of Litophyton sp. and Stereonephthya sp., with an average coverage of 958x and 890x, respectively ( Figure 2 ; Supplementary Figure S1). The mitogenomes of Litophyton sp. and Stereonephthya sp. were 19,130 bp and 18,912 bp in length, respectively. They encoded 14 protein-coding genes ( nad1 – 6, nad4l, cox1 – 3, atp6, atp8, cob , and mt-mutS ), two rRNA genes ( rrnS and rrnL ), and one tRNA gene ( trnM ) ( Figure 2 ). To date, 14 gene order patterns, recognized as patterns A–M and F1, have been discovered in Octocorallia ( Brockman and McFadden, 2012 ; Brugler and France, 2008 ; Hogan et al., 2019 ; Pante et al., 2013 ; Park et al., 2012 ; Poliseno et al., 2025 ; Uda et al., 2011 ; Yoshioka et al., 2025 ). The mitogenomes of Litophyton sp. and Stereonephthya sp. exhibited gene order pattern A, which is the most common pattern in Octocorallia. To examine its phylogenetic position of Litophyton sp. and Stereonephthya sp., we performed molecular phylogenetic analyses using publicly available mitogenomes of taxa belonging to Nephtheidae, as well as species phylogenetically closed taxa to this family. We aligned 18,674 nucleotide positions from 14 protein-coding genes and two rRNA genes. Litophyton sp. and Stereonephthya sp. collected in this study were clustered with other taxa belonging to family Nephtheidae ( Figure 3 ). The group of Litophyton sp. and Stereonephthya sp. was clustered with taxa belonging to genus Dendronephthya , the clade of which was sister to the genus Scleronephthya ( Figure 3 ). Download figure Open in new tab Figure 2. Mitogenome map of Litophyton sp. (A) and Stereonephthya sp. (B). Inner circles (grey) indicate GC contents. NADH dehydrogenase (yellow), ubichinol cytochrome c reductase (light-green), cytochrome c oxidase (pink), ATP synthase (green), tRNA (blue), rRNAs (red), and other gene (purple). Circular genomes were visualized with OGDRAW. Download figure Open in new tab Figure 3. Molecular phylogenetic tree for Litophyton and Stereonephthya based on complete mitogenomes. Rooted tree topology was estimated based on 18,674 nucleotide positions comprising 14 protein-coding genes and two rRNA genes. Litophyton sp. and Stereonephthya sp. are shown in red letter. Accession numbers for mitochondrial genomes are shown in parentheses after scientific names. Family names are shown in bold letter. Open circles indicate 100% bootstrap support (1,000 replicates). The bar indicates expected substitutions per site in aligned regions. Species used include the following: Ceeceenus quadrus NC_062003.1 ( Muthye et al., 2022 ), Eunephthya thyrsoidea NC_062010.1 ( Muthye et al., 2022 ), Dendronephthya castanea NC_023343.1 ( Park et al., 2012 ), Dendronephthya mollis NC_020456.1 ( Park et al., 2012 ), Dendronephthya suensoni NC_022809.1 ( Kwak et al., 2015 ), Scleronephthya gracillimum NC_023344.1 ( Park et al., 2012 ), and Acrophytum claviger NC_061990.1 ( Muthye et al., 2022 ). Discussion and Conclusion The phylogenetic relationships of Litophyton sp. and Stereonephthya sp. were congruent with the previous report based on ultra conserved elements ( McFadden et al., 2022 ). The complete mitogenomes presented here provides an important genomic resource for future studies of family Nephtheidae and octocoral mitogenome evolution. Ethical approval Ethical approval was not required for Litophyton sp. and Stereonephthya sp. in Okinawa, Japan. The sampling site is located outside of any protected area and ethical approval is not necessary. This study complies with the International Union for Conservation of Nature (IUCN) policies research involving species at risk of extinction (see Guidelines for appropriate uses of IUCN Red list data), the Convention on Biological Diversity, and the Convention on the Trade in Endangered Species of Wild Fauna and Flora. Funding This study was supported in part by Okinawa Prefecture Innovation / Ecosystem Joint Research Promotion Program. Disclosure statement The authors report there are no competing interests to declare. Data availability statement The mitogenomes for Litophyton sp. and Stereonephthya sp. are available in DDBJ/EMBL/GenBank under accession LC896078 and LC896077 , respectively. The associated BioProject, BioSample and SRA accession numbers for Litophyton sp. are PRJDB17996, SAMD01687581, and DRR752143, respectively. The associated BioProject, BioSample and SRA accession numbers for Stereonephthya sp. are PRJDB17996, SAMD01687582, and DRR752144, respectively. Author contribution (CRediT Role) Yuki Yoshioka: Formal analysis; Data curation; Writing – original draft Tatsuki Koido: Investigation Megumi Kanai: Funding acquisition; Investigation Noriyuki Satoh: Conceptualization; Funding acquisition; Writing – review & editing Tomofumi Nagata: Conceptualization; Funding acquisition Acknowledgments We thank members of the Sequencing Section at OIST for conducting genome sequencing, members of the Scientific Computing and Data Analysis section at OIST for computing resources. 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Share The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia) Yuki Yoshioka , Megumi Kanai , Tatsuki Koido , Noriyuki Satoh , Tomofumi Nagata bioRxiv 2025.10.14.682458; doi: https://doi.org/10.1101/2025.10.14.682458 Share This Article: Copy Citation Tools The complete mitochondrial genomes of Litophyton sp. and Stereonephthya sp., members of family Nephtheidae (Cnidaria: Anthozoa: Octocorallia) Yuki Yoshioka , Megumi Kanai , Tatsuki Koido , Noriyuki Satoh , Tomofumi Nagata bioRxiv 2025.10.14.682458; doi: https://doi.org/10.1101/2025.10.14.682458 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Genomics Subject Areas All Articles Animal Behavior and Cognition (7617) Biochemistry (17633) Bioengineering (13856) Bioinformatics (41840) Biophysics (21398) Cancer Biology (18529) Cell Biology (25422) Clinical Trials (138) Developmental Biology (13352) Ecology (19860) Epidemiology (2067) Evolutionary Biology (24281) Genetics (15582) Genomics (22461) Immunology (17700) Microbiology (40289) Molecular Biology (17138) Neuroscience (88413) Paleontology (666) Pathology (2823) Pharmacology and Toxicology (4813) Physiology (7632) Plant Biology (15107) Scientific Communication and Education (2042) Synthetic Biology (4283) Systems Biology (9807) Zoology (2267)