New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

Hasanuzzaman, Abul Farah Md.; Cao, Asunción; Ronza, Paolo; Fernández-Boo, Sergio; Rubiolo, Juan A.; Robledo, Diego; Gómez-Tato, Antonio; Álvarez‐Dios, José Antonio; Villalba, António; Martı́nez, Paulino

doi:10.1016/j.ijpara.2019.11.008

Cited by 6 publications

(2 citation statements)

References 104 publications

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“…In this regard, comparative analysis in the AQUAFAANG project will enlighten conserved and specific mechanisms of immune response regulation across different farmed fish lineages. Future studies in turbot should explore shorter periods following in vitro stimulation to provide further understanding of the head kidney response to viral and bacterial mimics, as done in other species (Hasanuzzaman et al, 2020;Herrera-Uribe et al, 2020). Upregulated DEGs shared by both in vivo stimulations were involved in the activation of transcription and translation and protein modification/localization.…”

Section: Transcriptomic Response To Immune Stimulationmentioning

confidence: 99%

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

Aramburu,

Gómez-Pardo,

Rodríguez-Villamayor

et al. 2024

Preprint

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Uncovering the epigenomic regulation of immune responses is essential for a comprehensive understanding of host defence mechanisms but remains poorly described in farmed fish. Here, we report the first annotation of the innate immune regulatory response in the genome of turbot (Scophthalmus maximus), a farmed flatfish. We integrated RNA-Seq with ATAC-Seq and ChIP-Seq (histone marks H3K4me3, H3K27ac and H3K27me3) using samples from head kidney. Sampling was performed 24 hours post-stimulation with viral (poly I:C) and bacterial (inactivate Vibrio anguillarum) mimics in vivo and in vitro (primary leukocyte cultures). Among the 8,797 differentially expressed genes (DEGs), we observed enrichment of transcriptional activation pathways in response to Vibrio and immune response pathways - including interferon stimulated genes - for poly I:C. Meanwhile, metabolic and cell cycle were downregulated by both mimics. We identified notable differences in chromatin accessibility (20,617 in vitro, 59,892 in vivo) and H3K4me3 bound regions (11,454 in vitro, 10,275 in vivo) - i.e. marking active promoters - between stimulations and controls. Overlaps of DEGs with promoters showing differential accessibility or histone mark binding revealed a significant coupling of the transcriptome and chromatin state. DEGs with activation marks in their promoters were enriched for similar functions to the global DEG set, but not in all cases, suggesting key regulatory genes were in poised or bivalent states. Active promoters and putative enhancers were differentially enriched in transcription factor binding motifs, many of them common to viral and bacterial responses. Finally, an in-depth analysis of immune response changes in chromatin state surrounding key DEGs encoding transcription factors was performed. This comprehensive multi-omics investigation provides an improved understanding of the epigenomic basis for the turbot immune responses and provides novel functional genomic information that can be leveraged in selective breeding towards enhanced disease resistance.

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Section: Transcriptomic Response To Immune Stimulationmentioning

confidence: 99%

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

Aramburu,

Gómez-Pardo,

Rodríguez-Villamayor

et al. 2024

Preprint

Self Cite

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“…Understanding the molecular basis of the differences responsible for being susceptible or resistant to a particular disease and identifying molecular markers of resistance can help to fight against mollusc diseases. Recently, research effort has been focused on the identification of molecular markers of disease resistance, through transcriptomics (He et al, 2012; Meistertzheim et al, 2014; Nikapitiya et al, 2014; Nie et al, 2015; Wang et al, 2016; Gutierrez et al, 2018, 2020; La Peyre et al, 2019; De Lorgeril et al, 2020; Farhat et al, 2020; Proestou and Sullivan, 2020; Hasanuzzaman et al, 2020), proteomics (Simonian et al, 2009; Fernández-Boo et al, 2016; de la Ballina et al, 2018; Vaibhav et al, 2018; Smits et al, 2020; Leprêtre et al, 2021) and population genomics approaches (Vera et al, 2019; Sambade et al, 2022). This information could be eventually used for marker-assisted selection (MAS) programs to increase resilience against pathogens.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome characterization of the common cockle (Cerastoderma edule) after exposure to aMarteilia cochilliaoutbreak

Pardo

Fernández

Pampin

et al. 2022

Preprint

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The edible cockle (Cerastoderma edule) is a widely cultivated bivalve with relevant ecological value roles and high value for shellfisheries in different European regions. The emergence of new threats, such as the parasiteMarteilia cochillia, has impaired the production and ecosystem of shellfish beds where the parasite was detected. Knowledge of the molecular mechanisms involved in cockle immune response to this parasite is essential to devise strategies for its control. With this aim, a transcriptomic study of the digestive gland (target organ of the parasite) and the whole cockle meat in response toM. cochilliainfection was carried out in heavily impacted area in the Northwest of Spain (Lombos do Ulla, Ria de Arousa). A total of 2079 million raw RNA-seq reads were obtained after filtering and used for annotation of 9049 genes following a conservative bioinformatic pipeline using the chromosome-level cockle genome as reference. Gene expression analysis identified a total of 973 consistent differentially expressed genes (DEGs) between comparisons across a temporal series involving cockles with different degrees of infection. DEGs increased with the level of infection within each temporal sample, but the higher DEGs number were detected when comparing temporal samples. Enrichment analysis of DEGs showed an increased expression of molecular functions related to hydrolase, peptidase activity, carbohydrate binding and active transmembrane transporter activity; cellular components such as extracellular matrix and extracellular regions; and a few biological functions associated with immunity and defence response. This information will be valuable for further studies focused on DEGs and associated SNP markers to develop reliant cockle strains to marteiliosis.

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Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams

Estêvão

Osório

Costas

et al. 2023

Fish & Shellfish Immunology

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New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

Abstract: New insights into the Manila clam-Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

Cited by 6 publications

References 104 publications

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

Transcriptome characterization of the common cockle (Cerastoderma edule) after exposure to aMarteilia cochilliaoutbreak

Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams

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