Mitochondrial gene rearrangement and phylogenetic relationships in the Amphilepidida and Ophiacanthida (Echinodermata, Ophiuroidea)

Lee, Taekjun; Bae, Yeon Jae; Shin, Sook

doi:10.1080/17451000.2019.1601226

Cited by 10 publications

(9 citation statements)

References 62 publications

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“…The O. brevispinum mitochondrial genome (mitogenome) is 15,831 bp long and has a GC content of 32.4% (Figure 5). These values are similar to those of the previously published [28] reference mitogenome of another brittle star species Ophiarachnella gorgonia (NCBI accession number NC 046053), which has a length of 15,948 bp and a GC content of 36.7%. Likewise, mitochondrial genome features of O. brevispinum showed the same gene order reported for O. gorgonia, and their putative control regions are of similar length (488 and 474 bp, respectively).…”

Section: Mitogenome Assemblysupporting

confidence: 88%

Twinkle twinkle brittle star, how I wonder what your genes are: Ophioderma brevispinum as a genomic resource for regeneration

Mashanov

Machado

Reid

et al. 2022

Preprint

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Background: Echinoderms are established models in experimental and developmental biology however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference experimtental studies of regenerative mechanisms. Results: We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,833 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration. Conclusions: The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration.

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Section: Mitogenome Assemblysupporting

confidence: 88%

Twinkle twinkle brittle star, how I wonder what your genes are: Ophioderma brevispinum as a genomic resource for regeneration

Mashanov

Machado

Reid

et al. 2022

Preprint

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“…The gene orders are identical to the two published mitogenomes from the same genus, further confirming the conservative gene order among congeners (Lee et al. 2019 ). Phylogeny inference with maximum likelihood robustly supports the monophyletic Amphiuridae but not to the genus Amphiura with Amphipholis squamata located between our species and Amphiura digitula .…”

supporting

confidence: 83%

“…However, very few studies have been published about Amphiura from deep sea (Hendler and Tran 2001). Recently, studies focussed on mitochondrial genome revealed that Ophiuroidea has undergone more complex gene rearrangements than other classes of echinoderms (Galaska et al 2019;Lee et al 2019). In this paper, the complete mitochondrial genome from a deep-sea Amphiura sp.…”

mentioning

confidence: 98%

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The complete mitochondrial genome of a deep sea ophiuroid of the genus Amphiura (Ophiuroidea: Amphiuridae)

Zhang

Cheng

et al. 2019

Mitochondrial DNA Part B

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Amphiura is a widely distributed genus of Ophiuroidea from various environment, play an important role in evolution. Here, we reported a complete mitochondrial genome of Amphiura sp. which was collected from a deep sea seamount in the West Pacific. The mitogenome is 15,457 in length, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. All genes are arranged in the same order of published mitogenomes in the same genus. The phylogenetic analysis support monophyly of the family Amphiuridae but not for the genus Amphiura.

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“…In particular, the remaining echinoderm classes, Ophiuroidea and Crinoidea, exhibit larger variations in gene order compared with their relatives in Echinodermata. Lee et al. (2019) examined 15 species of ophiuroid mitogenomes and found limited gene order conservation compared with asteroids, echinoids, and holothuroids, although the block of genes between cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6) were ordered identically among the four classes (see Scouras et al.…”

mentioning

confidence: 99%

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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Mitochondrial gene rearrangement and phylogenetic relationships in the Amphilepidida and Ophiacanthida (Echinodermata, Ophiuroidea)

Cited by 10 publications

References 62 publications

Twinkle twinkle brittle star, how I wonder what your genes are: Ophioderma brevispinum as a genomic resource for regeneration

Twinkle twinkle brittle star, how I wonder what your genes are: Ophioderma brevispinum as a genomic resource for regeneration

The complete mitochondrial genome of a deep sea ophiuroid of the genus Amphiura (Ophiuroidea: Amphiuridae)

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

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