Discovery and characterization of <i>Acanthamoeba castellanii</i> mitochondrial 5S rRNA

Bullerwell, Charles E.; Schnare, Murray N.; Gray, Michael W.

doi:10.1261/rna.2170803

Cited by 19 publications

(14 citation statements)

References 44 publications

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“…It is very diYcult to detect small RNAs because their function depends more on three-dimensional structure than on primary sequence conservation (e.g., Bullerwell et al 2003). However, we found the gene for a tmRNA (transfer-messenger RNA, Gueneau et al 1999; Gueneau de Novoa and Williams 2004) as well as the gene Vs encoding the chloroplast signal recognition particle RNA.…”

Section: General Features Of the Chloroplast Genomesmentioning

confidence: 76%

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

Grimwood²,

et al. 2007

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The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127-130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.

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Section: General Features Of the Chloroplast Genomesmentioning

confidence: 76%

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

Grimwood²,

et al. 2007

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“…The 5S rRNA, rps16 , and rpl19 genes in A. castellanii was annotated using the information published by Bullerwell et al. () and Gawryluk et al. ().…”

Section: Methodsmentioning

confidence: 99%

“…Boundaries of more divergent genes were verified using the Glimmer plugin for ORF prediction in Geneious and by translational alignment with the corresponding genes from the published genomes of the closely related amoebas. The 5S rRNA, rps16, and rpl19 genes in A. castellanii was annotated using the information published by Bullerwell et al (2003) and Gawryluk et al (2014). Genome maps were prepared using OGDRAW v1.2 (Lohse et al 2007) and Adobe Illustrator.…”

Section: Genome Annotationmentioning

confidence: 99%

Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences

Fučíková

Lahr

2015

J Eukaryotic Microbiology

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The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho-species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.

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“…The nuclear‐encoded cytoplasmic large subunit of the ribosome contains a 5S rRNA in Archaea, Bacteria and Eukaryota, and while chloroplast and plant mitochondria also have a 5S rRNA in their large ribosomal subunit, the mitochondria in fungi, animals and many protists do not (Bullerwell et al ., 2003). Our predicted structure of the nuclear‐encoded honey bee 5S rRNA (Fig.…”

mentioning

confidence: 99%

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

Gillespie¹,

Johnston²,

Cannone³

et al. 2006

Insect Molecular Biology

274

287

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As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

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Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA

Cited by 19 publications

References 44 publications

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

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