The complete mitochondrial genome of Hanabira yukibana Lau, Stokvis, Imahara & Reimer, 2019 (Cnidaria: Anthozoa: Octocorallia)

The complete mitochondrial genome of Hanabira yukibana Lau, Stokvis, Imahara & Reimer, 2019 (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 genome of Hanabira yukibana Lau, Stokvis, Imahara & Reimer, 2019 (Cnidaria: Anthozoa: Octocorallia) View ORCID Profile Yuki Yoshioka , Tatsuki Koido , Megumi Kanai , Shogo Gishitomi , Natsuki Watanabe , Noriyuki Satoh , Tomofumi Nagata doi: https://doi.org/10.1101/2025.09.27.678955 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.jpokikanka.or.jp Tatsuki Koido 2 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 Megumi Kanai 3 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 Shogo Gishitomi 3 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 Natsuki Watanabe 3 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 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 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 Abstract Full Text Info/History Metrics Preview PDF Abstract In this study, we sequenced the complete mitochondrial genome (mitogenome) of Hanabira yukibana (family Clavulariidae), collected in Okinawa, Japan. The complete mitochondrial genome of this specimen was 18,690 bp in length and contained 17 genes (14 protein-coding genes, two rRNA genes, and one tRNA gene). It exhibited gene order pattern A, which is the most common arrangement among octocorals. Molecular phylogenetic analysis indicated that H. yukibana is clustered with the genus Clavularia , including Clavularia inflata (the family Clavulariidae), consistent with the previous research using partial mitochondrial genes. Our study provides an additional mitochondrial genomic resource 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 (formerly known as Alcyonacea, Pennatulacea, or Helioporacea) ( 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 ). Hanabira yukibana Lau, Stokvis, Imahara & Reimer, 2019 , a member of the family Clavulariidae Hickson, 1894, was first described from Okinawa, Japan ( Lau et al., 2019 ). Similar to many shallow-reef octocorals, this species harbors symbiotic algae ( Lau et al., 2019 ). The genus name Hanabira (“petal” in Japanese) refers to the petal-like shape of the polyp tentacles, whereas the species name yukibana (“snow flower” in Japanese) alludes to the delicate sheen of the polyps. Because species identification in octocorals based solely on morphology remains challenging, genomic resources are indispensable for accurate taxonomic resolution. To date, mitogenome for this species have not been reported. In the present study, we report the complete mitogenome of H. yukibana and perform molecular phylogenetic analyses. Materials and Methods We collected a colony of H. yukibana in the reef slope (at 14.3 m in depth) near Yamakawa Port (latitude: 26.679029 and longitude: 127.880824), Okinawa-jima, Japan on 7 June 2024. A specimen was deposited at Kuroshio Biological Research foundation, Kochi, Japan (KBF) in the octocoral collection (OA) ( https://kuroshio.or.jp/ , contact parson: Tatsuki Koido, email: t.koido{at}kuroshio.or.jp ) under the voucher number “KBF-OA-00429”. Sample was preserved with 99.5% ethanol immediately after collection. Species was identified based on colony and polyp morphology, and observation of sclerites using scanning electron microscopy (JCM-7000 NeoScope™, JEOL Ltd.). Genomic DNA was extracted from the anthocodial 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 (New England Biolabs) according to the manufacturer’s protocol and were sequenced on an Illumina 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 missing annotations were manually curated. Complete mitogenome with gene annotation were visualized with OrganelleGenomeDRAW ( Greiner et al. 2019 ). We performed molecular phylogenetic analysis following Yoshioka et al. (2025) . The families Ideogorgiidae and Sarcodictyonidae belonging to Scleralcyonacea were used for outgroups. Results We successfully obtained the complete mitogenome of H. yukibana with an average coverage of 279x ( Figure 2 ). The mitogenome was 18,690 bp and 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 rearrangements, recognized as patterns A to 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 mitogenome of H. yukibana exhibited gene order pattern A, which is the most common arrangement in Octocorallia. To examine its phylogenetic position of H. yukibana , we performed molecular phylogenetic analyses using publicly available mitogenomes of taxa belonging to Clavulariidae, as well as species formerly assigned to this family. We aligned 18,524 nucleotide positions from 14 protein-coding genes and two rRNA genes. H. yukibana collected in this study was clustered with three Clavularia species (family Clavulariidae). Download figure Open in new tab Figure 1. A photograph of Hanabira yukibana . Photograph was taken by Tatsuki Koido. Download figure Open in new tab Figure 2. The complete mitochondrial genome of Hanabira yukibana and read coverage. (A) 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. (B) Coverage was calculated with BamDeal. The average depth is 279x. Discussion and Conclusion In this study, we reported first mitogenome of Hanabira yukibana . Overall, the phylogenetic relationships of H. yukibana were congruent with the previous report based on partial mitochondrial gene sets ( Lau et al., 2019 ). It is known that Clavularia crassa (NC_069554.1) is clustered with Paratelesto sp. (OL616258.1) (family Tubiporidae) ( Figure 3 ), due to the polyphyletic of the genus Clavularia reported previously ( McFadden et al., 2022 ; Yoshioka et al., 2025 ). The complete mitogenome presented here provides an important mitogenomic resource for future taxonomic studies of Clavulariidae and mitogenome evolution among octocorals. Download figure Open in new tab Figure 3. Molecular phylogenetic tree for Hanabira yukibana based on mitogenomes. Rooted tree topology was estimated based on 18,524 nucleotide positions comprising 14 protein-coding genes and two rRNA genes. Hanabira yukibana is shown in red letter. Accession numbers for mitochondrial genomes are shown in parentheses after scientific names. Open circles indicate 100% bootstrap support (1,000 replicates). The bar indicates expected substitutions per site in aligned regions. The families Ideogorgiidae and Sarcodictyonidae belong to the order Scleralcyonacea, while other families belong to the order Malacalcyonacea. Species used include the following: Clavularia inflata (NC_062006.1, Muthye et al., 2022 ), Clavularia sp. (MW166877.1), Clavularia sp. (LC831342.1, Yoshioka et al., 2025 ), Carijoa riisei (NC_048963.1, Easton and Hicks, 2020 ), Paratelesto sp. OL616258.1 ( Muthye et al.,2022 ), Phenganax marumi (PP330783.1, Poliseno et al., 2025 ), Phenganax stokvisi (PP330784.1, Poliseno et al., 2025 ), Phenganax subtilis (PP330785.1, Poliseno, et al., 2025 ), Incrustatus comauensis (MT254531.1, Poliseno et al., 2021 ), Telestula humilis (NC_073491.1, Poliseno et al., 2021 ), Trachythela sp. (MW238423.1, Zhou et al., 2021 ), Ideogorgia capensis (NC_062014.1, Muthye et al.,2022 ), Telestula septentrionalis (NC_073493.1, Poliseno et al., 2021 ), and Telestula cf. batoni (MT254530.1, Poliseno et al., 2021 ), and Clavularia crassa (NC_069554.1). 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 mitogenome is available in DDBJ/EMBL/GenBank under accession LC893425 . The associated BioProject, BioSample and SRA accession numbers are PRJDB17996, SAMD01681849, and DRR747072, respectively. CRediT Role Yuki Yoshioka: Formal analysis; Data curation; Writing – original draft Tatsuki Koido: Investigation Megumi Kanai: Funding acquisition; Investigation Shogo Gishitomi: Investigation Natsuki Watanabe: 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 and members of the Scientific Computing and Data Analysis section at OIST for computing resources. Funder Information Declared Okinawa Prefecture Innovation / Ecosystem Joint Research Promotion Program References ↵ Bernt M , Donath A , Jühling F , Externbrink F , Florentz C , Fritzsch G , Pütz J , Middendorf M , Stadler PF . 2013 . MITOS: improved de novo metazoan mitochondrial genome annotation . 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