Duplicated Rna Genes in Teleost Fish Genomes

Rose, Dominic; Jöris, Julian; Hackermüller, Jörg; Reiche, Kristin; Li, Qiang; Stadler, Peter F.

doi:10.1142/s0219720008003886

Cited by 13 publications

(16 citation statements)

References 38 publications

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“…As depicted in Figure 4A, 50% (16/32) of all donors and 94% (30/32) of all acceptors yield positive MaxEntScan scores implying that the sequence motifs of these sites are in agreement with known splice sites and therefore likely functional. Scoring the potential splice sites with a novel log-odds scoring scheme that evaluates substitution patterns of vertebrate splice sites and their ancestral sequences along a phylogenetic tree (Rose et al, 2011) yields −16.48 for EGO-B donors and 14.67 for EGO-B acceptors. Again, positive scores are indicative of functional splice sites.…”

Section: Resultsmentioning

confidence: 99%

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

Rose¹,

Stadler²

2011

Front. Gene.

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Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element.

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Section: Resultsmentioning

confidence: 99%

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

Rose¹,

Stadler²

2011

Front. Gene.

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“…Both C. demersum and H. verticillata are classified as fully immersed macrophytes (Rose et al, 2008).Therefore, oxygen concentration released in the water from photosynthesis process was higher than other macrophytes type such as floating types and emergent types.…”

Section: Discussionmentioning

confidence: 98%

“…Related aquatic plants are the primary producer of the food chain in a body of water. Macrophytes might contribute significantly the increase of dissolved oxygen concentration in the water and give benefits in increasing the productivity of an aquaculture activity through its ability to supply oxygen (Rose et al, 2008). Van et al (1976) stated that H. verticillata is able to perform photosynthesis process in short light intensity condition.…”

Section: Discussionmentioning

confidence: 99%

Identification and Classification of Lake Bottom Surface and Aquatic Vegetation in Laut Tawar Lake, Aceh

Fahmi

Husnah

2015

Indonesian Fisheries Research Journal

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Identification and classification of benthic habitats in Lake of Laut Tawar, Aceh by using hydro acoustic method can provide data and information on types of substrate and aquatic vegetation in a short time and wide spatial coverage, as done in the present work. Data acoustic collection was performed in 2013 using quantitative echosounder with split beam frequency of 120 kHz, and through a visual observation. The later is destined to look at the bottom types and macrophytes that lie on the line transect of acoustic survey. Analysis of data is to extract the value of bottom volume backscattering for each transect of 0.5-1 km. Classification of the bottom type was done based on the value of Sv using geospatial models. Results show the interval value of Sv for soft bottom ranged between -24.00 dB and -32.00 dB, the type of hard bottom (e.g. rocks, rocky sand substrate) ranged between -14.00 dB and -22.00 dB, whereas the Sv value of macrophyte ranged between-45.00 dB and -54.00 dB. The percent covers were about 42.90%, 44.71% and 12.93% for hard bottom type, soft bottom and macrophytes, respectively. The types of aquatic vegetation commonly found in the lake were two genera belonging Hydrocharitaceaea and Gramineae. The current work is still lack of information on the classification of organisms into genera scales. Therefore, more signal verification and algorithms verification would be needed in order to estimate macrophytes biomass by comparing with other visual observation.

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“…After all, a series of computational studies has provided quite convincing evidence for tens of thousands of unclassified RNAs whose secondary structure is under stabilizing selection (Missal et al, 2005;Rose et al, 2007;Torarinsson et al, 2006;Uzilov et al, 2006;Washietl et al, 2005Washietl et al, , 2007. Structure-based clustering Rose et al, 2008) furthermore strongly suggests that several new classes of ncRNAs with characteristic secondary structures are still lurking in eukaryotic genomes.…”

Section: Discussionmentioning

confidence: 99%