The complete mitochondrial genome of <i>Porites harrisoni</i> (Cnidaria: Scleractinia) obtained using next-generation sequencing

Terraneo, Tullia Isotta; Arrigoni, Roberto; Benzoni, Francesca; Forsman, Zac H.; Berumen, Michael L.

doi:10.1080/23802359.2018.1443852

Cited by 11 publications

(5 citation statements)

References 9 publications

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“…All three species exhibited a tRNA-met composed of 72 bp, yet the tRNA-trp gene varied in length from 70 bp (D. rotumana) to 71 bp (H. exesa and F. pentagona), with some subtle base composition difference between the species. Both tRNAs carried identical anticodons, as reported in other Scleractinia species (Niu et al, 2016;Terraneo et al, 2016a;Terraneo et al, 2016b). In addition, both tRNA genes were folded into typical cloverleaf secondary structures (Fig.…”

Section: Ribosomal and Transfer Rna Genessupporting

confidence: 70%

“…Mitochondrial genome rearrangements occur relatively infrequently within Scleractinia. The mitochondrial genome, therefore, played a significant role in scleractinian studies on phylogeny reconstruction (Fukami & Knowlton, 2005;Arrigoni et al, 2016;Capel et al, 2016;Terraneo et al, 2016a;Terraneo et al, 2016b). It could help us explore Scleractinia's evolutionary process and clarify the evolutionary relationship between Scleractinia and other Hexacorallia members, such as Actiniaria, Antipatharia, and Corallimorpharia (Fukami & Knowlton, 2005;Kitahara et al, 2014;Lin et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

Niu

Xiao

Tian

et al. 2020

PeerJ

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Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.

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Section: Ribosomal and Transfer Rna Genessupporting

confidence: 70%

Section: Introductionmentioning

confidence: 99%

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

Niu

Xiao

Tian

et al. 2020

PeerJ

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“…Mito‐nuclear discordance here may be indicative of a problem during the RAD data analysis or an evolutionary process responsible for the incongruity such as introgression (reviewed in Ballard & Whitlock, 2004). To our knowledge, few studies have attempted to mine the mitochondrial data present in RAD data sets for independent analysis (but see Marrano et al, 2017; Perry, Pederson, & Baxter, 2017; Pujolar et al, 2014; Terraneo, Arrigoni, Benzoni, Forsman, & Berumen, 2018; Truong et al, 2012). Here, we compare results from our previous genome‐wide SNP study of KwaZulu‐Natal yellowfish (Stobie et al, 2018) with analyses of mitochondrial SNP markers mined from the ddRAD sequence data.…”

Section: Introductionmentioning

confidence: 99%

Finding stories in noise: Mitochondrial portraits from RAD data

Stobie

Cunningham

Oosthuizen

et al. 2018

Molecular Ecology Resources

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Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years; however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy next-generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many single nucleotide polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses.

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“…2019 ; this study), and even as by-products of restriction site-associated DNA ( Terraneo et al. 2018 a, 2018 b) or hybrid-capture ( Allio et al. 2020 ; Quek et al.…”

mentioning

confidence: 74%

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

Quek

Chang

et al. 2020

Molecular Biology and Evolution

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The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analysed 23 Asteroidea mitogenomes, including 10 newly-sequenced species, and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids and holothuroids, with only an interchange between two gene positions in asteroids over approximately 500 million years of echinoderm evolution.

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The complete mitochondrial genome of Porites harrisoni (Cnidaria: Scleractinia) obtained using next-generation sequencing

Cited by 11 publications

References 9 publications

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics

Finding stories in noise: Mitochondrial portraits from RAD data

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

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