Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Uda, Kouji; Komeda, Yusuke; Fujita, Toshihiko; Iwasaki, Naohiko; Bavestrello, Giorgio; Giovine, Marco; Cattaneo‐Vietti, Riccardo; Suzuki, Tomohiko

doi:10.1016/j.cbd.2013.05.003

Cited by 18 publications

(17 citation statements)

References 34 publications

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“…The observed absence of RNA-Seq reads in G. ventalina supports this proposition. The presence of very similar stem-loop structure in the ND6-COI IGR in C. rubrum, along with absence of RNA-Seq reads in this region of this species, suggests that this IGR is the potential CR in octocorals with "C" type mitogenome arrangement and corroborates earlier predictions in this regard [32,49] (Additional file 3).…”

Section: Discussionsupporting

confidence: 87%

“…Additionally, RNA-Seq data from two published octocoral transcriptome studies were screened for mitochondrial reads. These included Gorgonia ventalina (Genome arrangement A; SRX177804-5) and Corallium rubrum (Genome arrangement C; SRX675792) [31,[47][48][49]. Hence, they provided us with the opportunity to explore mt-transcription in octocorals with different mitogenome arrangements.…”

Section: Recovering Mitogenomic Transcripts From Rna-seq Data Of S Cmentioning

confidence: 99%

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Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Shimpi

Vargas

Poliseno

et al. 2017

Preprint

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Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density and content, gene orders, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results:We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions (UTRs) of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, mtMutS, was found to undergo alternative polyadenylation (APA), and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected.Conclusions: Mt-mRNA processing in octocorals bearing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represents a first step towards understanding its functional and evolutionary implications.

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Section: Discussionsupporting

confidence: 87%

Section: Recovering Mitogenomic Transcripts From Rna-seq Data Of S Cmentioning

confidence: 99%

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Shimpi

Vargas

Poliseno

et al. 2017

Preprint

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“…The comparison with previous results on P. japonicum and C. konojoi (Uda et al 2011) supports the validity of a classification separating the Coralliidae family into the two genera, but not as proposed by Bayer and Cairns (2003). Considering the gene order arrangement and the nucleotide sequence identity, Uda et al (2013) found that Corallium rubrum is closer to Paracorallium japonicum than Corallium elatius and Corallium konojoi and concluded that the currently accepted generic classification of Coralliidae must be reconsidered (Uda et al 2013).…”

Section: Discussionmentioning

confidence: 98%

“…Moreover on the basis of molecular sequencing and phylogenetic analyses, Ardila et al (2012) concluded that there was no support for the taxonomic status of the two currently recognized genera in the Coralliidae family. To clarify the systematic positions of Corallium and Paracorallium species, Uda et al (2013) determined the complete mitochondrial genome sequence of C. elatius and C. rubrum. The comparison with previous results on P. japonicum and C. konojoi (Uda et al 2011) supports the validity of a classification separating the Coralliidae family into the two genera, but not as proposed by Bayer and Cairns (2003).…”

Section: Discussionmentioning

confidence: 99%

Block-by-block and layer-by-layer growth modes in coral skeletons

Perrin

Vielzeuf

Ricolleau

et al. 2015

American Mineralogist

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Understanding the dynamics of biomineral growth is a challenging goal of biomineralogy that can be achieved in part by deciphering biomineral structures and chemistries. The morphology, structure, and chemistry of six skeletons of Corallium and Paracorallium species (C. rubrum, C. elatius, C. johnsoni, C. niobe, P. japonicum, and P. thrinax) from the Mediterranean, the Atlantic, and the Pacific oceans have been studied by X-ray micro-computed tomography, polarized light microscope, scanning electron microscope, and electron microprobe. All species have two types of biomineral structures: an inner skeleton and sclerites that are small grains of Mg-calcite found in the living tissues surrounding the skeleton. All skeletons display a central core surrounded by an annular domain. In the species studied by electron microprobe (C. rubrum, C. elatius, and P. japonicum), the central core and the annular domains display different chemical compositions with the core richer in magnesium and poorer in sulfur than the annular domain. In terms of structure, special emphasis has been put on central cores for which little data are available. The central cores are made of sclerites and sclerite aggregates within a cement consisting of fine layers of Mg-calcite. On the other hand, the annular parts are made of fine concentric layers of calcite crystallites with only rare sclerites. These contrasting features imply two different growth modes: (1) a "block and cement" mode taking place at the apex of a branch and associated with a fast axial growth rate (~2 mm/yr); and (2) a layer-by-layer mode occurring below the apex and associated with a slow radial growth (~0.2 mm/yr). The change from a growth mode to another is anatomically controlled by the presence of a continuous network of gastrodermal canals around the sub-apical skeleton, preventing to a large extent the aggregation of sclerites. It is generally accepted that the Coralliidae family exhibits different types of skeletogeneses. In contrast with this idea, we observe that all studied Corallium species display remarkable similarities in terms of skeletogenesis and a unifying growth model for the Corallium genus is proposed. Similarities and differences with previous models are discussed. The present study shows that the morphological criterion initially used to establish the genus Paracorallium in the Coralliidae family is inadequate.

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“…Moreover, this study, together with the work by Pante et al (2014) in the octocoral genus Chrysogorgia, constitute the first applications of RADsequencing for phylogenetics and species delimitation in cnidarians. Only a handful of previous studies, using traditional mitochondrial data and the ITS2 and 28S nuclear markers, have attempted to evaluate phylogenetic relationships in the octocoral AC clade (Herrera et al 2010;Ardila et al 2012;Brockman & McFadden 2012;Herrera et al 2012;McFadden & van Ofwegen 2013;Uda et al 2013;Figueroa & Baco 2014). These studies find support for the monophyly of the genus Paragorgia, the family Coralliidae, and the sister relationship between the Paragorgiidae and Coralliidae.…”

Section: Rad Sequencing Enables Unprecedented Phylogenetic Resolutionmentioning

confidence: 99%

Evolutionary and ecological genomics in deep-sea organisms

Monroy¹

2015

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Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. AKNOWLEDGEMENTSThis degree is the fulfillment of a lifelong dream. I am infinitely grateful to Tim Shank, for taking a chance with me, for challenging me constantly, for honest advising, for providing limitless opportunities to pursue my interests and develop my skills, for unconditional support and trust, and for making me feel more like a colleague than a student since the first day. I could not imagine a better place to have done my PhD. I look forward to many more ventures to come. I am extremely grateful to my committee ...

show abstract

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Cited by 18 publications

References 34 publications

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Block-by-block and layer-by-layer growth modes in coral skeletons

Evolutionary and ecological genomics in deep-sea organisms

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