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Suárez-Castillo, Edna C.; García‐Arrarás, José E.

doi:10.1186/1471-2148-7-23

Cited by 41 publications

(25 citation statements)

References 66 publications

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“…More recently however, a number of Epd paralogues have been identified in a variety of other vertebrate organs, particularly those of fish, although their functions are largely unknown [53]. Here, we identify that at least one Epd gene is constitutively expressed in kidney, heart, and skeletal muscle of Sockeye salmon but not in peripheral blood (Fig.…”

Section: Discussionmentioning

confidence: 70%

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

et al. 2016

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BackgroundPiscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state. We further investigate the role of PRV as a coinfecting agent following superinfection with infectious hematopoietic necrosis virus (IHNV) – a highly pathogenic rhabdovirus endemic to the west coast of North America.ResultsChallenge of Sockeye salmon with PRV resulted in high quantities of viral transcripts to become present in the blood and kidney of infected fish without manifestations of disease. De novo transcriptome assembly of over 2.3 billion paired RNA-seq reads from the head kidneys of 36 fish identified more than 320,000 putative unigenes, of which less than 20 were suggested to be differentially expressed in response to PRV at either 2 or 3 weeks post challenge by DESeq2 and edgeR analysis. Of these, only one, Ependymin, was confirmed to be differentially expressed by qPCR in an expanded sample set. In contrast, IHNV induced substantial transcriptional changes (differential expression of > 20,000 unigenes) which included transcripts involved in antiviral and inflammatory response pathways. Prior infection with PRV had no significant effect on host responses to superinfecting IHNV, nor did host responses initiated by IHNV exposure influence increasing PRV loads.ConclusionsPRV does not substantially alter the head kidney transcriptome of Sockeye salmon during early (2 to 3 week) infection and dissemination in a period of significant increasing viral load, nor does the presence of PRV change the host transcriptional response to an IHNV superinfection. Further, concurrent infections of PRV and IHNV do not appear to significantly influence the infectivity or severity of IHNV associated disease, or conversely, PRV load.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3196-y) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 70%

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

et al. 2016

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“…Bayesian analysis did not reach convergence after 30 million generations, and therefore the results must be treated with caution. The poor support is not unexpected given the low degree of overall sequence conservation among EPDR sequences [ 10 ]. The analyses did separate EPDR protein sequences into two major clades, with some support (maximum likelihood ML bootstrap value 14, Bayesian posterior probability 74%).…”

Section: Resultsmentioning

confidence: 99%

“…It was within this context that Suárez-Castillo and García-Arrarás conducted the first systematic analysis of EPDRs in animals, aided by the growing availability of expressed sequence tag (EST) projects [ 10 ]. Not only did they detect EPDRs in non-deuterostome bilaterians, they also identified additional piscine EPDRs that were expressed in non-brain tissues.…”

Section: Introductionmentioning

confidence: 99%

The evolution of ependymin-related proteins

et al. 2018

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BackgroundEpendymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood.ResultsWe undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar.ConclusionsOur results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.

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“…Eviscerated animals were let to regenerate for 3, 5, 7, 10, and 14 days before the dissection and tissue extraction. For the dissection, organisms were anesthetized by placement in ice-cold water for 1 h. [1,3,9]. Dissected tissues were rinsed in ice-cold filtered seawater and processed for RNA isolation.…”

Section: Methodsmentioning

confidence: 99%

Characterization of two novel EF-hand proteins identifies a clade of putative Ca²⁺-binding protein specific to the Ambulacraria

Soto-Acabá

Ortíz-Pineda

García‐Arrarás

2020

Preprint

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In recent years, transcriptomic databases have become one of the main sources for protein discovery. In our studies of nervous system and digestive tract regeneration in echinoderms, we have identified several transcripts that have attracted our attention. One of these molecules corresponds to a previously unidentified transcript (Orpin) from the sea cucumber Holothuria glaberrima that appeared to be upregulated during intestinal regeneration. We have now identified a second highly similar sequence and analyzed the predicted proteins using bioinformatics tools. Both sequences have EF-hand motifs characteristic of calcium-binding proteins (CaBPs) and N-terminal signal peptides. Sequence comparison analyses such as multiple sequence alignments and phylogenetic analyses only showed significant similarity to sequences from other echinoderms or from hemichordates. Semi-quantitative RT-PCR analyses revealed that transcripts from these sequences are expressed in various tissues including muscle, haemal system, gonads, and mesentery. However, contrary to previous reports, there was no significant differential expression in regenerating tissues. Nonetheless, the identification of unique features in the predicted proteins suggests that these might comprise a novel subfamily of EF-hand containing proteins specific to the Ambulacraria clade.

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Cited by 41 publications

References 66 publications

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

The evolution of ependymin-related proteins

Characterization of two novel EF-hand proteins identifies a clade of putative Ca²⁺-binding protein specific to the Ambulacraria

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Untitled

Cited by 41 publications

References 66 publications

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

The evolution of ependymin-related proteins

Characterization of two novel EF-hand proteins identifies a clade of putative Ca2+-binding protein specific to the Ambulacraria

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Characterization of two novel EF-hand proteins identifies a clade of putative Ca²⁺-binding protein specific to the Ambulacraria