Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish <i>Alatina alata</i> (Cnidaria: Medusozoa: Cubozoa)

<p>Background: In most animals, the mitochondrial genome is characterized by its small size, organization into a single circular molecule, and a relative conservation of the number of encoded genes. In box jellyfish (Cubozoa, Cnidaria), the mitochondrial genome is organized into 8 linear mito-chromosomes harboring between one and 4 genes each, including 2 extra protein-coding genes: <i>mt-polB</i> and <i>orf314</i>. Such an organization challenges the traditional view of mitochondrial DNA (mtDNA) expression in animals. In this study, we investigate the pattern of mitochondrial gene expression in the box jellyfish <i>Alatina alata</i>, as well as several key nuclear-encoded molecular pathways involved in the processing of mitochondrial gene transcription. Results: Read coverage of DNA-seq data is relatively uniform for all 8 mito-chromosomes, suggesting that each mito-chromosome is present in equimolar proportion in the mitochondrion. Comparison of DNA and RNA-seq based assemblies indicates that mito-chromosomes are transcribed into individual transcripts in which the beginning and ending are highly conserved. Expression levels for <i>mt-polB</i> and <i>orf314</i> are similar to those of other mitochondrial-encoded genes, which provides further evidence for them having functional roles in the mitochondrion. Survey of the transcriptome suggests recognition of the mitochondrial tRNA-Met by the cytoplasmic aminoacyl-tRNA synthetase counterpart and C-to-U editing of the cytoplasmic tRNA-Trp after import into the mitochondrion. Moreover, several mitochondrial ribosomal proteins appear to be lost. Conclusions: This study represents the first survey of mitochondrial gene expression of the linear multi-chromosomal mtDNA in box jellyfish (Cubozoa). Future exploration of small RNAs and the proteome of the mitochondrion will test the hypotheses presented herein.</p

Putative scheme of the life cycle of <i>H. antarcticus</i>, including the “microhydrula” phase.

<p>The main life cycle was based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski1" target="_blank">[6]</a>, for <i>H. octoradiatus</i>. Stauropolyp stage and its ability to create frustules (white arrows) are hypothesized based on observations of <i>Stylocoronella </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Kikinger1" target="_blank">[7]</a>. Dotted gray arrows corresponding to the “microhydrula” stage, derived from this study. Figures modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Kikinger1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Jarms1" target="_blank">[11]</a>.</p

Intraspecific variation for three species of Staurozoa in 16S, ITS1 and ITS2, highlighting the number of specimens, the number of haplotypes found and the range of divergence of each molecular marker; the linear distance refers to the distance between populations.

<p>Intraspecific variation for three species of Staurozoa in 16S, ITS1 and ITS2, highlighting the number of specimens, the number of haplotypes found and the range of divergence of each molecular marker; the linear distance refers to the distance between populations.</p

Map of Antarctica and southernmost part of Chile.

<p>Stars are records of <i>Haliclystus antarcticus</i>: South Georgia Island, Paulet Island, King George Island (Polish “Arctowski” Station, US “Copacabana” Refuge and Argentinean Antarctic Station “Jubany”) and Chile (Valdivia).</p

Living specimens of <i>Haliclystus antarcticus</i> in the field.

<p>A and B) Side view, attached to rock; C) Side view attached to rock and algae (Rhodophyta <i>Iridaea cordata</i>). Pictures from Morandini, AC. Scale = 1.2 cm.</p

Phylogenetic hypothesis (MP) based on mitochondrial 16S, nuclear ITS1+ITS2 and combined data.

<p>AN (King George Island, Antarctica), AK (Akkeshi, Hokkaido, Japan), CA (Franklin Point, California, USA), CH (Valdivia, Chile), MU (Muroran, Hokkaido, Japan), WA (San Juan Island, Washington, USA).“1” and “2” refers to the different haplotypes found for each species. Bootstrap indices under both MP and ML (respectively) at each node. Topologies are congruent under MP and ML analysis.</p

Comparisons between the <i>M. limopsicola</i> polyp and the <i>H. octoradiatus</i> settled planula.

<p><i>(A–C) different stages of M. limopsicola </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Jarms1" target="_blank">[11]</a>: A) newly settled “polyp”; B) closely attached “polyps”, with expansions provided with nematocysts; C) later stage, with a cauliflower-shaped head. <i>(D–E) process of frustulation observed in both species</i>: D) planula of <i>H. octoradiatus</i> producing lateral protuberances, which become frustules <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski1" target="_blank">[6]</a>; E) frustules <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Jarms1" target="_blank">[11]</a>. <i>(F–G) possible correspondences of stages of both species</i>: F) a group of <i>H. octoradiatus</i> larvae, capturing a nauplius <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski1" target="_blank">[6]</a>; G) superior view of a settled planula of <i>H. octoradiatus</i> at an advanced stage, showing four lobes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski2" target="_blank">[8]</a>.The hemispherical shape and the production of frustules (A, D, E) are similar in settled planulae of <i>H. octoradiatus</i> and “polyps” of <i>M. limopsicola</i>. The same gregarious behavior to feeding was observed in both species (B, F). At a more advanced stage, the larva of <i>H. octoradiatus</i> presents four lobes (G), that might be associated with the cauliflower structure seen in later stages of <i>M. limopsicola</i> (C), which possibly is an aggregation of more than one individual. Figures modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Wietrzykowski2" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010182#pone.0010182-Jarms1" target="_blank">[11]</a>.</p

Localities, GenBank codes (*sequences produced in this study) and number of specimens used in molecular analysis for each species and for each molecular marker.

<p>Localities, GenBank codes (*sequences produced in this study) and number of specimens used in molecular analysis for each species and for each molecular marker.</p

DNA distance matrix between <i>Haliclystus antarcticus</i> from Antarctica and: “<i>Microhydrula limopsicola</i>”, <i>Haliclystus antarcticus</i> from Chile, <i>Haliclystus</i> “<i>sanjuanensis</i>”, <i>Haliclystus stejnegeri</i>, <i>Haliclystus tenuis</i>, <i>Depastromorpha africana</i> (family Depastridae) and <i>Lucernaria janetae</i> (family Lucernariidae).

<p>DNA distance matrix between <i>Haliclystus antarcticus</i> from Antarctica and: “<i>Microhydrula limopsicola</i>”, <i>Haliclystus antarcticus</i> from Chile, <i>Haliclystus</i> “<i>sanjuanensis</i>”, <i>Haliclystus stejnegeri</i>, <i>Haliclystus tenuis</i>, <i>Depastromorpha africana</i> (family Depastridae) and <i>Lucernaria janetae</i> (family Lucernariidae).</p

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