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Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
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Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
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Quattrini AM, Snyder KE, Purow-Ruderman R, Seiblitz IGL, Hoang J, Floerke N, Ramos NI, Wirshing HH, Rodriguez E, McFadden CS. Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes. Sci Rep 2023; 13:7443. [PMID: 37156831 PMCID: PMC10167242 DOI: 10.1038/s41598-023-34059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.
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Affiliation(s)
- Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA.
| | - Karen E Snyder
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | | | - Isabela G L Seiblitz
- Centre for Marine Biology, University of São Paulo, São Sebastião, 11612-109, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Natasha Floerke
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Herman H Wirshing
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Estefanía Rodriguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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Ramos NI, DeLeo DM, Horowitz J, McFadden CS, Quattrini AM. Selection in coral mitogenomes, with insights into adaptations in the deep sea. Sci Rep 2023; 13:6016. [PMID: 37045882 PMCID: PMC10097804 DOI: 10.1038/s41598-023-31243-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/08/2023] [Indexed: 04/14/2023] Open
Abstract
Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean's surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject to selection pressures at greater depths to meet the metabolic demands of that environment. Here, we use a phylogenomic framework combined with codon-based models to evaluate whether mt protein-coding genes (PCGs) associated with cellular energy functions are under positive selection across depth in three groups of corals: Octocorallia, Scleractinia, and Antipatharia. The results demonstrated that mt PCGs of deep- and shallow-water species of all three groups were primarily under strong purifying selection (0.0474 < ω < 0.3123), with the exception of positive selection in atp6 (ω = 1.3263) of deep-sea antipatharians. We also found evidence for positive selection at fifteen sites across cox1, mtMutS, and nad1 in deep-sea octocorals and nad3 of deep-sea antipatharians. These results contribute to our limited understanding of mt adaptations as a function of depth and provide insight into the molecular response of corals to the extreme deep-sea environment.
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Affiliation(s)
- Nina I Ramos
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Danielle M DeLeo
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Jeremy Horowitz
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | | | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
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Seiblitz IGL, Vaga CF, Capel KCC, Cairns SD, Stolarski J, Quattrini AM, Kitahara MV. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol Phylogenet Evol 2022; 175:107565. [PMID: 35787457 DOI: 10.1016/j.ympev.2022.107565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.
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Affiliation(s)
- I G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil.
| | - C F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, PL-00-818 Warsaw, Poland
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - M V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil.
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Valenti I, Degradi L, Kunova A, Cortesi P, Pasquali M, Saracchi M. The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family. FRONTIERS IN FUNGAL BIOLOGY 2022; 2:802511. [PMID: 37744111 PMCID: PMC10512376 DOI: 10.3389/ffunb.2021.802511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 09/26/2023]
Abstract
Ciborinia camelliae is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus Camellia, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of Ciborinia camellia is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (rps3) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of C. camelliae. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.
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Affiliation(s)
| | | | | | | | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
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The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny. Life (Basel) 2021; 11:life11050402. [PMID: 33924866 PMCID: PMC8146996 DOI: 10.3390/life11050402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/15/2023] Open
Abstract
A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.
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Seiblitz IGL, Capel KCC, Stolarski J, Quek ZBR, Huang D, Kitahara MV. The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. Sci Rep 2020; 10:20714. [PMID: 33244171 PMCID: PMC7693180 DOI: 10.1038/s41598-020-77763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/11/2020] [Indexed: 11/08/2022] Open
Abstract
Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
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Affiliation(s)
- Isabela G L Seiblitz
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
| | - Kátia C C Capel
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | | | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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Poliseno A, Santos MEA, Kise H, Macdonald B, Quattrini AM, McFadden CS, Reimer JD. Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology Laboratory Graduate School of Engineering and Science University of the Ryukyus Nishihara Japan
| | - Maria Eduarda Alves Santos
- Molecular Invertebrate Systematics and Ecology Laboratory Graduate School of Engineering and Science University of the Ryukyus Nishihara Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology Laboratory Graduate School of Engineering and Science University of the Ryukyus Nishihara Japan
| | | | - Andrea M. Quattrini
- Department of Biology Harvey Mudd College Claremont CA USA
- Department of Invertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington, DC USA
| | | | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory Graduate School of Engineering and Science University of the Ryukyus Nishihara Japan
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
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Corsaro D, Venditti D. Putative group I introns in the eukaryote nuclear internal transcribed spacers. Curr Genet 2019; 66:373-384. [PMID: 31463775 DOI: 10.1007/s00294-019-01027-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/17/2019] [Indexed: 11/28/2022]
Abstract
Group I introns are mobile genetic elements that interrupt genes encoding proteins and RNAs. In the rRNA operon, introns can insert in the small subunit (SSU) and large subunit (LSU) of a wide variety of protists and various prokaryotes, but they were never found in the ITS region. In this study, unusually long ITS regions of fungi and closely related unicellular organisms (Polychytrium aggregatum, Mitosporidium daphniae, Amoeboaphelidium occidentale and Nuclearia simplex) were analysed. While the insertion of repeats is responsible for long ITS in other eukaryotes, the increased size of the sequences analysed herein seems rather due to the presence of introns in ITS-1 or ITS-2. The identified insertions can be folded in secondary structures according to group I intron models, and they cluster within introns in conserved core-based phylogeny. In addition, for Mitosporidium, Amoeboaphelidium and Nuclearia, more conventional ITS-2 structures can be deduced once spacer introns are removed. Sequences of five shark species were also analysed for their structure and included in phylogeny because of unpublished work reporting introns in their ITS, obtaining congruent results. Overall, the data presented herein indicate that spacer regions may contain introns.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS, 12 rue du Maconnais, Vandoeuvre-lès-Nancy, 54500, France.
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10
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Chi SI, Dahl M, Emblem Å, Johansen SD. Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Mol Biol 2019; 20:16. [PMID: 31153363 PMCID: PMC6545197 DOI: 10.1186/s12867-019-0134-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 05/23/2019] [Indexed: 01/29/2023] Open
Abstract
Background The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. Results We obtained the complete mitochondrial genome sequences and corresponding mitochondrial transcriptomes of the two distantly related corallimorpharian species Ricordea yuma and Amplexidiscus fenestrafer. All mitochondrial genes were found to be expressed at the RNA-level. Both introns were perfectly removed by autocatalytic splicing, but COI-884 excision appeared more efficient than ND5-717. ND5-717 was organized into giant group I intron elements of 18.1 kb and 19.3 kb in A. fenestrafer and R. yuma, respectively. The intron harbored almost the entire mitochondrial genome embedded within the P8 peripheral segment. Conclusion ND5-717 was removed by group I intron splicing from a small primary transcript that contained a permutated intron–exon arrangement. The splicing pathway involved a circular exon-containing RNA intermediate, which is a hallmark of RNA back-splicing. ND5-717 represents the first reported natural group I intron that becomes excised by back-splicing from a permuted precursor RNA. Back-splicing may explain why Corallimorpharia mitochondrial genomes tolerate giant group I introns. Electronic supplementary material The online version of this article (10.1186/s12867-019-0134-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway. .,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
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11
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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. [PMID: 29366757 DOI: 10.1016/j.gene.2018.01.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/19/2017] [Accepted: 01/19/2018] [Indexed: 11/16/2022]
Abstract
The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function.
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Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ilona Urbarova
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway; Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
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12
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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] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/03/2017] [Accepted: 07/10/2017] [Indexed: 11/20/2022]
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