Appendix - Advances in the Studies of the Benthic Zone

In January 2020 about 200 hexacoral mitochondrial genomes have been completely, or nearly completely, sequenced. These mitochondrial genomes repre- sent all 5 hexacoral orders, 51 families, 77 genera, and 133 distinct species. All specimens (100%) harbor ND5-717 and approximately 50% harbor COI introns.

Key features are summarized in Appendix Table 1.

Advances in the Studies of the Benthic Zone

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 A:Seaanemones(OrderActiniaria) SynhalcuriaselegansActiniaridaeKR051009P11,445bpND5+(1635bp)COI ActiniaequinaActiniidaeMH545699C20,690bpND5+(2170bp)884_COI+(857bp) ActiniatenebrosaActiniidaeMK291977C20,691bpND5+(2170bp)884_COI+(854bp) AnemoniamajanoActiniidaeKY860670C19,545bpND5+(1679bp)884_COI+(853bp) AnemoniasulcataActiniidaeMN011067C20,390bpND5+(1725bp)884_COI+(1053bp) AnemoniaviridisActiniidaeKY860669C20,108bpND5+(1726bp)884_COI+(853bp) AnthopleuramidoriActiniidaeKT989511C20,039bpND5+(1714bp)884_COI+(854bp) BoloceratuediaeActiniidaeHG423145C19,143bpND5+(2055bp)884_COI+(853bp) Bolocerasp.ActiniidaeKU507297C19,463bpND5+(2397bp)884_COI+(854bp) EntacmaeaquadricolorActiniidaeMN066616C20,960bpND5+(2052bp)884_COI+(853bp) EpiactisjaponicaActiniidaeMN076184C18,835bpND5+(1681bp)884_COI+(853bp) EpiactisproliferaActiniidaeRef.[33]C19,752bpND5+(1737bp)884_COI+(853bp) IsosicyonisstriataActiniidaeKR051006C19,001bpND5+(1695bp)884_COI+(853bp) UrticinaequesActiniidaeHG423144C20,458bpND5+(1681bp)884_COI+(850bp) AntholobaachatesActinostolidaeKR051002C17,816bpND5+(1884bp)884_COI+(853bp) StomphiaselaginellaActinostolidaeRef.[33]C18,349bpND5+(1784bp)884_COI+(829bp) Aiptasiapulchella4AiptasiidaeHG423147C19,791bpND5+(1730bp)884_COI+(847bp) Aiptasiapulchella4AiptasiidaeHG423148C19,790bpND5+(1730bp)884_COI+(847bp) BartholomeaannulataAiptasiidaeMN066614C19,615bpND5+(1754bp)884_COI+(847bp) AliciasansibarensisAliciidaeKR051001C19,575bpND5+(2158bp)COI RelicanthusdaphneaeBoloceroididaeMK947129C17,727bpND5+(1721bp)884_COI+(926bp) Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

significant lower expressions. This is observed for COI-884 introns of Hormathia and Anemonia sea anemones [12, 15], COI-884 introns of mushroom corals [16], and COI-867 introns of colonial anemones [14].

5. Concluding remarks

A hallmark of hexacoral mitochondrial genomes is the presence of self-catalytic group I introns. What is the biological role of these mitochondrial introns—are they purely selfish genetic elements, or could they have gained new regulatory functions beyond self-splicing? Current knowledge suggests a fungal origin of the hexacoral introns [19, 34, 49]. The group I introns in the COI gene encode LAGLIDADG-type homing endonucleases, consistent with intron mobility between cognate intron-less alleles [12, 45]. The hexacoral COI introns appear gained and lost in multiple cycles during the last 0.5 billion years [42], which supports a selfish intron behavior.

The ND5-717 intron is apparently obligatory in hexacoral mitochondrial genomes, making this genetic element an interesting candidate in gene regulation.

Similar obligatory group I introns have been noted in the chloroplast tRNA^Leugene of all green plants and in the nuclear LSU rRNA gene of all Physarales myxomycetes [50, 51]. These obligatory mitochondrial, chloroplast, and nuclear introns are con- sidered domesticated group I introns that may have gained new host-specific functions beyond self-splicing [21, 25]. The mitochondrial ND5 mRNA stability has a key role in respiratory control in higher animals; it is tightly regulated and contains m¹A base modification [52–54]. Intron retention of ND5 mRNA was recently reported in mushroom corals [16], suggesting possible host regulatory functions in hexacorals. Thus, further investigations on hexacoral mitochondrial intron functions and biological roles are needed and highly welcome.

Acknowledgements

We thank current and former members of the research teams at the Genomics Group (Nord University) and the RNA Group (UiT—The Arctic University of Norway) for discussion and support. A special thanks to the former PhD students Sylvia Ighem Chi and Ilona Urbarova for thoroughly investigating hexacoral genomics.

Conflict of interest

The authors declare that they have no conflict of interest.

A. Appendix

Key features are summarized in Appendix Table 1.

Advances in the Studies of the Benthic Zone

DOI: http://dx.doi.org/10.5772/intechopen.91465

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 EdwardsiagilbertensisEdwardsiidaeMN066615P17,661bpND5+(1604bp)COI EdwardsiatimidaEdwardsiidaeRef.[33]C18,683bpND5+(1622bp)COI Nematostellasp.EdwardsiidaeDQ643835C16,389bpND5+(1620bp)COI ProtantheasimplexGonactiniidaeMH500774/75C21,326bpND5+(15,262bp)COI HalcampoidespurpureaHalcampoidisaeKR051003C18,038bpND5+(1648bp)884_COI+(856bp) HalcuriaspilatusHalcuriidaeKR051004P10,972bpND5+(1635bp)COI HaloclavaproductaHaloclavidaeMN076185P17,416bpND5+(1681bp)884_COI+(853bp) HormathiadigitataHormathiidaeHG423146C18,754bpND5+(1681bp)884_COI+(853bp) LiponemabrevicorneLiponematidaeMN076188C19,143bpND5+(2055bp)884_COI+(853bp) MetridiumsenileMetridiidaeHG423143C17,444bpND5+(1681bp)884_COI+(853bp) MetridiumsenileMetridiidaeAF000023C17,743bpND5+(1681bp)884_COI+(853bp) PhymanthuscruciferPhymanthidaeKR051007C19,727bpND5+(1911bp)884_COI+(865bp) SagartiaornataSagartiidaeKR051008C17,446bpND5+(1671bp)884_COI+(853bp) HeteractisauroraStichodactylidaeMN076186C19,999bpND5+(1737bp)884_COI+(853bp) HeteractiscrispaStichodactylidaeMN076187C18,835bpND5+(1681bp)884_COI+(853bp) StichodactylahelianthusStichodactylidaeRef.[33]C19,551bpND5+(1681bp)884_COI+(866bp) StichodactylahelianthusStichodactylidaeUnpublished5C18,999bpND5+(1680bp)884_COI+(865bp) StichodactylameretensiiStichodactylidaeRef.[33]C18,849bpND5+(1681bp)884_COI+(866bp) B:Colonialanemones(OrderZoantharia) SavaliasavagliaParazoanthidaeDQ825686C20,764bpND5+(2052bp)867_COI+(1238bp) PalythoaheliodiscusSphenopidaeKY888673C20,841bpND5+(2077bp)887_COI+(1276bp) ZoanthussansibaricusZoanthidaeKY888672C20,972bpND5+(2096bp)867_COI+(1327bp) Advances in the Studies of the Benthic Zone

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 C:Mushroomcorals(OrderCorallimorpharia) CorallimorphusprofundusCorallimorphidaeKP938440C20,488bpND5+(12,389bp)884_COI+(1182bp) CorynactiscalifornicaCorallimorphidaeKP938436C20,715bpND5+(10,531bp)884_COI+(1265bp) Pseudocorynactissp.CorallimorphidaeKP938437C21,239bpND5+(18,840bp)884_COI+(1177bp) AmplexidiscusfenestraferDiscosomatidaeMH308002C20,054bpND5+(17,960bp)884_COI+(1206bp) AmplexidiscusfenestraferDiscosomatidaeKP938435C20,188bpND5+(18,094bp)884_COI+(1206bp) DiscosomanummiformeDiscosomatidaeKP938434C20,925bpND5+(18,791bp)884_COI+(1208bp) Discosomasp.DiscosomatidaeDQ643965C20,908bpND5+(18,803bp)884_COI+(1207bp) Discosomasp.DiscosomatidaeDQ643966C20,912bpND5+(19,807bp)884_COI+(1206bp) Discosomasp.DiscosomatidaeMH308003C20,288bpND5+(18,196bp)884_COI+(1206bp) RhodactisindosinensisDiscosomatidaeKP938438C20,100bpND5+(18,013bp)884_COI+(1204bp) RhodactismussoidesDiscosomatidaeKP938439C20,826bpND5+(18,721bp)884_COI+(1206bp) Rhodactissp.DiscosomatidaeDQ640647C20,093bpND5+(18,001bp)884_COI+(1206bp) RicordeafloridaRicordeidaeDQ640648C21,376bpND5+(19,247bp)884_COI+(1176bp) RicordeayumaRicordeidaeMH308004C21,430bpND5+(19,301bp)884_COI+(1198bp) RicordeayumaRicordeidaeMH308005C21,566bpND5+(19,437bp)884_COI+(1198bp) RicordeayumaRicordeidaeKP938441C22,015bpND5+(19,886bp)884_COI+(1198bp) D:Blackcorals(OrderAntipatharia) Cirrhipatheslutkeni6AntipathidaeJX023266C20,448bpND5+(2062bp)884_COI+(1439bp) MyriopathesjaponicaAntipathidaeJX456459C17,733bpND5+(1699bp)884_COI+(924bp) ChrysopathesformosaCladopathidaeDQ304771C18,398bpND5+(1932bp)COI Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 E:Stonycorals(OrderScleractinia) Complexclade AcroporaaculeusAcroporidaeKT001202C18,528bpND5+(12,116bp)COI AcroporaacuminataAcroporidaeLC201815C18,586bpND5+(12,175bp)COI AcroporaasperaAcroporidaeKF448532C18,479bpND5+(12,070bp)COI AcroporaausteraAcroporidaeLC201816C18,346bpND5+(11,937bp)COI AcroporaawiAcroporidaeLC201849C18,478bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201850C18,479bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201851C18,479bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201852C18,479bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201853C18,479bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201854C18,479bpND5+(12,070bp)COI AcroporaawiAcroporidaeLC201855C18,479bpND5+(12,070bp)COI AcroporacarduusAcroporidaeLC201813C18,373bpND5+(11,964bp)COI AcroporacarduusAcroporidaeLC201814C18,372bpND5+(11,963bp)COI AcroporacythereaAcroporidaeLC201817C18,568bpND5+(12,158bp)COI AcroporacythereaAcroporidaeLC201818C18,567bpND5+(12,157bp)COI AcroporacythereaAcroporidaeLC201819C18,568bpND5+(12,158bp)COI AcroporadigitiferaAcroporidaeKF448535C18,479bpND5+(12,070bp)COI AcroporadivaricataAcroporidaeKF448537C18,481bpND5+(12,072bp)COI AcroporaechinataAcroporidaeLC201820C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201821C18,480bpND5+(12,071bp)COI Advances in the Studies of the Benthic Zone

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 AcroporaechinataAcroporidaeLC201822C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201823C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201824C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201825C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201826C18,482bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201834C18,481bpND5+(12,072bp)COI AcroporaechinataAcroporidaeLC201835C18,368bpND5+(11,959bp)COI AcroporaechinataAcroporidaeLC201836C18,482bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201837C18,368bpND5+(11,959bp)COI AcroporaechinataAcroporidaeLC201838C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201839C18,482bpND5+(12,073bp)COI AcroporaechinataAcroporidaeLC201840C18,480bpND5+(12,071bp)COI AcroporaechinataAcroporidaeLC201841C18,367bpND5+(11,958bp)COI AcroporafloridaAcroporidaeKF448533C18,365bpND5+(11,956bp)COI AcroporafloridaAcroporidaeLC201827C18,365bpND5+(11,956bp)COI AcroporagrandisAcroporidaeLC201828C18,479bpND5+(12,070bp)COI AcroporahorridaAcroporidaeKF448530C18,480bpND5+(12,071bp)COI AcroporahumilisAcroporidaeKF448528C18,479bpND5+(12,070bp)COI AcroporahyacinthusAcroporidaeKF448531C18,566bpND5+(12,157bp)COI AcroporahyacinthusAcroporidaeLC201829C18,567bpND5+(12,157bp)COI AcroporahyacinthusAcroporidaeLC201830C18,567bpND5+(12,157bp)COI AcroporahyacinthusAcroporidaeLC201831C18,567bpND5+(12,157bp)COI Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 AcroporahyacinthusAcroporidaeLC201832C18,568bpND5+(12,158bp)COI AcroporaintermediaAcroporidaeLC201833C18,479bpND5+(12,070bp)COI AcroporamicrophthalmaAcroporidaeLC201842C18,479bpND5+(12,070bp)COI AcroporamicrophthalmaAcroporidaeLC201843C18,481bpND5+(12,072bp)COI AcroporamuricataAcroporidaeKF448529C18,481bpND5+(12,072bp)COI AcroporamuricataAcroporidaeLC201844C18,480bpND5+(12,071bp)COI AcroporanasutaAcroporidaeKF448536C18,481bpND5+(12,072bp)COI AcroporanasutaAcroporidaeLC201845C18,374bpND5+(11,965bp)COI AcroporanasutaAcroporidaeLC201846C18,484bpND5+(12,074bp)COI AcroporarobustaAcroporidaeKF448538C18,480bpND5+(12,071bp)COI AcroporaselagoAcroporidaeLC201847C18,482bpND5+(12,073bp)COI AcroporaselagoAcroporidaeLC201848C18,480bpND5+(12,071bp)COI AcroporatenuisAcroporidaeAF338425C18,338bpND5+(11,928bp)COI AcroporatenuisAcroporidaeLC201856C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201857C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201858C18,343bpND5+(11,934bp)COI AcroporatenuisAcroporidaeLC201859C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201860C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201861C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201862C18,343bpND5+(11,934bp)COI AcroporatenuisAcroporidaeLC201863C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201864C18,342bpND5+(11,933bp)COI Advances in the Studies of the Benthic Zone

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 AcroporatenuisAcroporidaeLC201865C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201866C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201867C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201868C18,342bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201869C18,341bpND5+(11,933bp)COI AcroporatenuisAcroporidaeLC201870C18,342bpND5+(11,933bp)COI AcroporavalidaAcroporidaeMH141598C18,385bpND5+(11,976bp)COI AcroporayongeiAcroporidaeKF448534C18,342bpND5+(11,933bp)COI AnacroporamatthaiAcroporidaeAY903295C17,888bpND5+(11,492bp)COI AstreoporaexplanataAcroporidaeKJ634269C18,106bpND5+(11,795bp)COI AstreoporamyriophthalmaAcroporidaeKJ634272C18,106bpND5+(11,795bp)COI MontiporacactusAcroporidaeAY903296C17,887bpND5+(11,485bp)COI MontiporaaequituberculataAcroporidaeKU762339C17,886bpND5+(11,488bp)COI MontiporaefflorescensAcroporidaeMG851914C17,886bpND5+(11,491bp)COI AgariciafragilisAgariciidaeKM051016C18,667bpND5+(11,525bp)COI AgariciahumilisAgariciidaeDQ643831C18,735bpND5+(11,536bp)COI PavonaclavusAgariciidaeDQ643836C18,315bpND5+(11,129bp)COI PavonadecussataAgariciidaeKP231535C18,378bpND5+(11,129bp)COI DendrophylliaarbusculaDendrophyllidaeKR824937C19,069bpND5+(11,299bp)884_COI+(964bp) DendrophylliacribrosaDendrophyllidaeJQ290080C19,072bpND5+(11,282bp)884_COI+(964bp) TubastraeacoccineaDendrophyllidaeKX024566C19,094bpND5+(11,322bp)884_COI+(964bp) TubastraeacoccineaDendrophyllidaeJQ290078C19,070bpND5+(11,300bp)884_COI+(964bp) Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 TubastraeatagusensisDendrophyllidaeKX024567C19,094bpND5+(11,324bp)884_COI+(964bp) TurbinariapeltataDendrophyllidaeKJ725201C18,966bpND5+(11,332bp)884_COI+(964bp) EuphylliaancoraEuphylliidaeJF825139C18,875bpND5+(11,866bp)COI GalaxeafascicularisEuphylliidaeKU159433C18,751bpND5+(12,022bp)COI FungiacyathusstephanusFungiacyathidaeJF825138C19,381bpND5+(10,932bp)COI+(961bp) AlveoporajaponicaPoritidaeMG851913C18,144bpND5+(11,621bp)COI Alveoporasp.PoritidaeKJ634271C18,146bpND5+(11,621bp)COI GonioporacolumnaPoritidaeJF825141C18,766bpND5+(11,175bp)884_COI+(964bp) PoritesfontanesiiPoritidaeNC_037434C18,658bpND5+(11,131bp)884_COI+(965bp) PoritesharrisoniPoritidaeNC_037435C18,630bpND5+(11,133bp)884_COI+(965bp) PoriteslobataPoritidaeKU572435C18,647bpND5+(11,133bp)884_COI+(965bp) PoritesluteaPoritidaeKU159432C18,646bpND5+(11,130bp)884_COI+(971bp) PoritesokinawensisPoritidaeJF825142C18,647bpND5+(11,133bp)884_COI+(965bp) PoritespanamensisPoritidaeKJ546638C18,628bpND5+(11,117bp)884_COI+(965bp) PoritesporitisPoritidaeDQ643837C18,648bpND5+(11,135bp)884_COI+(965bp) PoritesrusPoritidaeLN864762C18,647bpND5+(11,133bp)884_COI+(971bp) PseudosiderastreaformosaSiderastreidaeKP260632C19,475bpND5+(11,524bp)884_COI+(970bp) PseudosiderastreatayamiSiderastreidaeKP260633C19,475bpND5+(11,524bp)884_COI+(970bp) SiderastrearadiansSiderastreidaeDQ643838C19,387bpND5+(11,463bp)884_COI+(988bp) Robustclade MadracisdecactisAstrocoeniidaeKX982259C16,970bpND5+(10,435bp)COI MadracismirabilisAstrocoeniidaeEU400212C16,951bpND5+(10,415bp)COI Advances in the Studies of the Benthic Zone

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 Lopheilapertusa7CaryophyllidaeFR821799C16,150bpND5+(6460bp)COI Lopheliapertusa7CaryophyllidaeKC875348C16,149bpND5+(6460bp)COI Lopheliapertusa7CaryophyllidaeKC875349C16,149bpND5+(6460bp)COI SolenosmiliavariabilisCaryophyllidaeKM609293C15,968bpND5+(6459bp)COI SolenosmiliavariabilisCaryophyllidaeKM609294C15,968bpND5+(6459bp)COI ColpopyllianatansFlaviidaeDQ643833C16,906bpND5+(10,445bp)COI PlesiastreaversiporaFlaviidaeMH025639C15,320bpND5+(9398bp)COI EchinophylliaasperaLobophylliidaeMG792550C17,697bpND5+(10,136bp)720_COI+(1077bp) Sclerophylliamaxima8LobophylliidaeFO904931C18,168bpND5+(10,760bp)720_COI+(1074bp) DipsastraearotumanaMerulinidaeMH119077C16,466bpND5+(10,149bp)COI FlaviteshalicoraMerulinidaeMH794283C17,033bpND5+(11,150bp)COI HydnoporaexesaMerulinidaeMH086217C17,790bpND5+(10,243bp)COI OrbicellaannularisMerulinidaeAP008973C16,138bpND5+(9540bp)COI OrbicellaannularisMerulinidaeAP008974C16,138bpND5+(9540bp)COI OrbicellafaveolataMerulinidaeAP008977C16,138bpND5+(9540bp)COI OrbicellafaveolataMerulinidaeAP008978C16,138bpND5+(9540bp)COI OrbicellafranksiMerulinidaeAP008975C16,138bpND5+(9540bp)COI OrbicellafranksiMerulinidaeAP008976C16,137bpND5+(9539bp)COI Polycyathussp.MerulinidaeJF825140C15,357bpND5+(9438bp)COI PlatygyracarnosaMerulinidaeJX911333C16,463bpND5+(10,164bp)COI MussaangulosaMussidaeDQ643834C17,245bpND5+(10,636bp)COI MadreporaoculataOculinidaeJX236041C15,841bpND5+(10,140bp)COI Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

SpeciesFamilyAccessionnoMtsize1ND5intron(size)2COIintron(size)3 PocilloporadamicornisPocilloporidaeEU400213C17,425bpND5+(10,864bp)COI PocilloporadamicornisPocilloporidaeEF526302C17,415bpND5+(10,863bp)COI PocilloporaeydouxiPocilloporidaeEF526303C17,422bpND5+(10,863bp)COI SeriatoporacaliendrumPocilloporidaeEF633601C17,010bpND5+(10,467bp)COI SeriatoporahystrixPocilloporidaeEF633600C17,059bpND5+(10,465bp)COI StylophorapistillataPocilloporidaeEU400214C17,177bpND5+(10,583bp)COI Astrangiasp.RhizangiidaeDQ643832C14,853bpND5+(9258bp)COI 1Sizeofmitochondrialgenome.C,completelysequenced;P,partial/almostcompletelysequenced. 2SizeofND5-717groupIintron. 3SizeofCOIgroupIintron.COI,noCOIintronpresent;720,867,or884intronsindicated. 4TheseaanemoneAiptasiapulcellamayalsobeannotatedasExaiptasiapallida. 5InformationfromourunpublishedcompletemitochondtialgenomesequenceofStichodactylahelianthus. 6TheblackcoralCirrhipatheslutkenimayalsobeannotatedasStrichpateslutkeni. 7ThestonycoralLopheliapertusamayalsobeannotatedasDesmophyllumpertusum. 8ThestonycoralSclerophylliamaximamayalsobeannotatedasAcanthastreamaxima. AppendixTable1. KeyfeaturesofgroupIintronsinhexacoralmitogenomes.

Advances in the Studies of the Benthic Zone

Author details

Steinar Daae Johansen¹* and Åse Emblem²

1 Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway

2 Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway

*Address all correspondence to: [email protected]

by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements DOI: http://dx.doi.org/10.5772/intechopen.91465

Advances in the Studies of the Benthic Zone

Author details

Steinar Daae Johansen¹* and Åse Emblem²

1 Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway

2 Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway

*Address all correspondence to: [email protected]

by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements DOI: http://dx.doi.org/10.5772/intechopen.91465

References

[1]Daly M, Brugler MR, Cartwright P, Collins AG, Dawson MN, Fautin DG, et al. The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus. Zootaxa. 1668;

2007:127-182. Available from: www.

mapress.com/zootaxa/

[2]Stampar SN, Maronna MM,

Kitahara MV, Reimer JD, Morandini AC.

Fast-evolving mitochondrial DNA in Ceriantharia: A reflection of hexacorallia paraphyly? PLoS One. 2014;9:e86612.

DOI: 10.1371/journal.pone.0086612 [3]Roberts JM, Wheeler AJ, Freiwald A.

Reefs of the deep: The biology and geology of cold-water coral ecosystems.

Science. 2006;312:543-547. DOI:

10.1126/science.1119861

[4]Daly M. Boloceroides daphneae, a new species of giant sea anemone (Cnidaria:

Actiniaria: Boloceroididae) from the deep Pacific. Marine Biology. 2006;148:

1241-1247. DOI: 10.1007/s00227-005- 0170-7

[5]Zhang B, Zhang Y-H, Wang X, Zhang H-X, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp.

exhibits novel genetic structures

potentially involved in adaptation to the deep-sea environment. Ecology and Evolution. 2017;7:4951-4962. DOI:

10.1002/ece3.3067

[6]Dubin A, Chi SI, Emblem Å, Moum T, Johansen SD. Deep-water sea anemone with a two-chromosome mitochondrial genome. Gene. 2019;692:195-200. DOI:

10.1016/j.gene.2018.12.074

[7]Roberts JM, Wheeler AJ, Freiwald A, Cairns S. Cold-water Corals: The Biology and Geology of Deep-sea Coral Habitats.

New York: Cambridge University Press;

2009. ISBN: 978-0-521-88485-3 [8]Buhl-Mortensen L, Buhl-Mortensen P. Cold Temperature Coral Habitats,

Corals in a Changing World, CD Beltran and ET Camacho. Rijeka: IntechOpen;

2018. DOI: 10.5772/intechopen.71446 [9]Friedman JR, Nunnari J.

Mitochondrial form and function.

Nature. 2014;505:335-343. DOI:

10.1038/nature12985

[10]Anderson AJ, Jackson TD, Stroud DA, Stojanovski D.

Mitochondria—Hubs for regulating cellular biochemistry: Emerging concepts and networks. Open Biology. 2019;9:

190126. DOI: 10.1098/rsob.190126 [11]Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B. Mitogenomics at the base of Metazoa. Molecular Phylogenetics and Evolution. 2013;69:

339-351. DOI: 10.16/j.ympev.2013.07.016 [12]Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, et al.

Sea anemones possess dynamic mitogenome structures. Molecular Phylogenetics and Evolution. 2014;75:

184-193. DOI: 10.1016/j.ympev.2014.

02.016

[13]Flot JF, Tillier S. The mitochondrial genome of Pocillopora (Cnidaria:

Scleractinia) contains two variable regions:

The putative D-loop and a novel ORF of unknown function. Gene. 2007;401:80-87.

DOI: 10.1016/j.gene.2007.07.006 [14]Chi SI, Johansen SD. Zoantharian mitochondrial genomes contain unique complex group I introns and highly conserved intergenic regions. Gene.

2017;628:24-31. DOI: 10/1016/j.gene.

2017.07.023

[15]Chi SI, Urbarova I, Johansen SD.

Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes:

Lesson learned from Anemonia viridis.

Gene. 2018;652:78-86. DOI: 10.1016/j.

gene.2018.01.067 Advances in the Studies of the Benthic Zone

[16]Chi SI, Dahl M, Emblem Å, Johansen SD. Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Molecular Biology. 2019;20:16. DOI: 10.1186/

s12867-019-0134-y

[17]Beagley CT, Okada NA,

Wolstenholme DR. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: One intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proceedings of the National Academy of Sciences of the United States of America. 1996;93:

5619-5623. DOI: 10.1073/ pnas.93.11.5619

[18]Johansen SD, Emblem Å,

Karlsen BO, Okkenhaug S, Hansen H, Moum T, et al. Approaching marine bioprospecting in hexacorals by RNA deep sequencing. New Biotechnology.

2010;27:267-275. DOI: 10.1016/j.

nbt.2010.02.019

[19]Emblem Å, Karlsen BO, Evertsen J, Johansen SD. Mitogenome

rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long- term evolving group I intron. Molecular Phylogenetics and Evolution. 2011;61:

495-503. DOI: 10.1016/j. ympev.2011.07.012

[20]Beagley CT, Wolstenholme DR.

Characterization and localization of mitochondrial DNA-encoded tRNA and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile. Current Genetics. 2013;59:139-152. DOI:

10.1007/s00294-013-0395-9

[21]Nielsen H, Johansen SD. Group I introns: Moving in new directions. RNA Biology. 2009;6:375-383. DOI: 10.4161/

rna.6.4.9334

[22]Schuster A, Lopez JV, Becking LE, Kelly M, Pomponi SA, Worheide G, et al. Evolution of group I introns in Porifera: New evidence for intron

mobility and implications for DNA barcoding. BMC Evolutionary Biology. 2017;17:82. DOI: 10.1186/s12862-017- 0928-9

[23]Cech TR, Damberger SH, Gutell RR. Representation of the secondary and tertiary structure of group I introns. Nature Structural Biology. 1994;1: 273-280. DOI: 10.1038/nsb0594-273 [24]Vicens Q, Cech TR. Atomic level architecture of group I introns revealed. Trends in Biochemical Sciences. 2006; 31:41-51. DOI: 10.1016/j.

tibs.2005.11.008

[25]Hedberg A, Johansen SD. Nuclear group I introns in self-splicing and beyond. Mobile DNA. 2013;4:17. DOI: 10.1186/1759-8753-4-17

[26]Jørgensen TE, Johansen SD. Expanding the coding potential of vertebrate mitochondrial genomes: Lesson learned from the Atlantic cod. In: Seligmann H, editor. Mitochondrial DNA—New Insight. Rijeka:

IntechOpen; 2018. DOI: 10.5772/ intechopen.75883

[27]Kühlbrandt W. Structure and function of mitochondrial membrane protein complexes. BMC Biology. 2015; 13:89. DOI: 10.1186/s12915-015-0201-x [28]Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. Naked corals: Skeleton loss in Scleractinia.

Proceedings of the National Academy of Sciences of the United States of

America. 2006;103:9096-9100. DOI: 10.1073/pnas.0602444103

[29]Sinniger F, Chevaldonne P, Pawlowski J. Mitochondrial genome of Savalia savaglia (Cnidaria, Hexacorallia) and early metazoan phylogeny. Journal of Molecular Evolution. 2007;64:196-203. DOI: 10.1007/s00239-006-0015-0 [30]Lin MF, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, et al. Mitochondrial Group I Introns in Hexacorals Are Regulatory Genetic Elements

DOI: http://dx.doi.org/10.5772/intechopen.91465

Dalam dokumen Advances in the Studies of the Benthic Zone (Halaman 119-135)