scholarly journals First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4449 ◽  
Author(s):  
Jan D. Brüwer ◽  
Christian R. Voolstra
Keyword(s):  
Genetic Material ◽  
Model System ◽  
Rna Seq ◽  
Sequencing Data ◽  
Viral Origin ◽  
Viral Community ◽  
Coral Reef Ecosystems ◽  
Algal Endosymbiont ◽  
Multicellular Organisms ◽  
Insight Into

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.

scholarly journals Insights into viral community composition of the cnidarian model metaorganism Aiptasia using RNA-Seq data

2017 ◽  
Author(s):  
Jan D Brüwer ◽  
Christian R Voolstra
Keyword(s):  
Community Composition ◽  
Well Being ◽  
Rna Seq ◽  
Viral Origin ◽  
Viral Community ◽  
Coral Reef Ecosystems ◽  
Algal Endosymbiont ◽  
Endosymbiotic Algae ◽  
Multicellular Organisms ◽  
Insight Into

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems and their well-being strongly relies on forming mutualistic relationships with endosymbiotic algae of the genus Symbiodinium. So far, only few studies characterized viral diversity and the potential underlying functional importance to coral holobionts. Here we analyzed an existing RNA-Seq dataset of the coral model metaorganism Aiptasia CC7 (sensu Exaiptasia pallida) associated with aposymbiotic, partially populated, and fully symbiotic anemones with Symbiodinium to gain further insight into viral community composition and the relation to the algal endosymbiosis. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (~ 3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences (paired-end read pairs) could be assigned as of viral origin. Taxonomic annotation shows that Aiptasia is associated with a diverse viral community consisting of 116 viral taxa covering 40 families. The viral community was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral community, we found that some viral taxa significantly changed in relative abundance when Aiptasia engage in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present in all samples revealed an Aiptasia core virome of 15 viral taxa from 11 viral families that was comprised of many viruses previously reported in coral viromes. Our study provides a first insight into the viral community of Aiptasia. Aiptasia seem to harbor a diverse and overall stable viral community, although certain members change in abundance when the anemone host associates with its algal endosymbiont. However, the functional significance of this remains to be determined.

scholarly journals Insights into viral community composition of the cnidarian model metaorganism Aiptasia using RNA-Seq data

2017 ◽  
Author(s):  
Jan D Brüwer ◽  
Christian R Voolstra
Keyword(s):  
Community Composition ◽  
Well Being ◽  
Rna Seq ◽  
Viral Origin ◽  
Viral Community ◽  
Coral Reef Ecosystems ◽  
Algal Endosymbiont ◽  
Endosymbiotic Algae ◽  
Multicellular Organisms ◽  
Insight Into

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems and their well-being strongly relies on forming mutualistic relationships with endosymbiotic algae of the genus Symbiodinium. So far, only few studies characterized viral diversity and the potential underlying functional importance to coral holobionts. Here we analyzed an existing RNA-Seq dataset of the coral model metaorganism Aiptasia CC7 (sensu Exaiptasia pallida) associated with aposymbiotic, partially populated, and fully symbiotic anemones with Symbiodinium to gain further insight into viral community composition and the relation to the algal endosymbiosis. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (~ 3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences (paired-end read pairs) could be assigned as of viral origin. Taxonomic annotation shows that Aiptasia is associated with a diverse viral community consisting of 116 viral taxa covering 40 families. The viral community was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral community, we found that some viral taxa significantly changed in relative abundance when Aiptasia engage in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present in all samples revealed an Aiptasia core virome of 15 viral taxa from 11 viral families that was comprised of many viruses previously reported in coral viromes. Our study provides a first insight into the viral community of Aiptasia. Aiptasia seem to harbor a diverse and overall stable viral community, although certain members change in abundance when the anemone host associates with its algal endosymbiont. However, the functional significance of this remains to be determined.

A role of SAND-family proteins in endocytosis

2005 ◽  
Vol 33 (4) ◽  
pp. 606-608 ◽  
Author(s):  
D. Poteryaev ◽  
A. Spang
Keyword(s):  
Caenorhabditis Elegans ◽  
Membrane Trafficking ◽  
Reverse Genetics ◽  
Model System ◽  
Loss Of Function ◽  
C Elegans ◽  
Eukaryotic Species ◽  
Multicellular Organisms ◽  
Insight Into

Caenorhabditis elegans has recently been used as an attractive model system to gain insight into mechanisms of endocytosis in multicellular organisms. A combination of forward and reverse genetics has identified a number of new membrane trafficking factors. Most of them have mammalian homologues which function in the same transport events. We describe a novel C. elegans gene sand-1, whose loss of function causes profound endocytic defects in many tissues. SAND-1 belongs to a conserved family of proteins present in all eukaryotic species, whose genome is sequenced. However, SAND family has not been previously characterized in metazoa. Our comparison of C. elegans SAND-1 and its yeast homologue, Mon1p, showed a conserved role of the SAND-family proteins in late steps of endocytic transport.

scholarly journals Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research

2017 ◽  
Author(s):  
Pradipta Ray ◽  
Andrew Torck ◽  
Lilyana Quigley ◽  
Andi Wangzhou ◽  
Matthew Neiman ◽  
...  
Keyword(s):  
Chronic Pain ◽  
Rna Sequencing ◽  
Dorsal Root Ganglia ◽  
Dorsal Root ◽  
Expression Patterns ◽  
Rna Seq ◽  
Sequencing Data ◽  
Mouse Tissues ◽  
Human And Mouse ◽  
Insight Into

AbstractMolecular neurobiological insight into human nervous tissues is needed to generate next generation therapeutics for neurological disorders like chronic pain. We obtained human Dorsal Root Ganglia (DRG) samples from organ donors and performed RNA-sequencing (RNA-seq) to study the human DRG (hDRG) transcriptional landscape, systematically comparing it with publicly available data from a variety of human and orthologous mouse tissues, including mouse DRG (mDRG). We characterized the hDRG transcriptional profile in terms of tissue-restricted gene co-expression patterns and putative transcriptional regulators, and formulated an information-theoretic framework to quantify DRG enrichment. Our analyses reveal an hDRG-enriched protein-coding gene set (~140), some of which have not been described in the context of DRG or pain signaling. A majority of these show conserved enrichment in mDRG, and were mined for known drug - gene product interactions. Comparison of hDRG and tibial nerve transcriptomes suggest pervasive mRNA transport of sensory neuronal genes to axons in adult hDRG, with potential implications for mechanistic insight into chronic pain in patients. Relevant gene families and pathways were also analyzed, including transcription factors (TFs), g-protein coupled receptors (GCPRs) and ion channels. We present our work as an online, searchable repository (http://www.utdallas.edu/bbs/painneurosciencelab/DRGtranscriptome), creating a valuable resource for the community. Our analyses provide insight into DRG biology for guiding development of novel therapeutics, and a blueprint for cross-species transcriptomic analyses.SummaryWe generated RNA sequencing data from human DRG samples and comprehensively compared this transcriptome to other human tissues and a matching panel of mouse tissues. Our analysis uncovered functionally enriched genes in the human and mouse DRG with important implications for understanding sensory biology and pain drug discovery.

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