run_metadata: 19149

This data as json

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19149	ERR14086576	ERX13488950	ERS21188940	ERP165174	PRJEB81327	A comparison of the immunological response in zebrafish and rainbow trout infected with fish parasite Ichthyophthirius multifiliis	420c6801-49a8-433c-9e91-52e1fc6cc95a	Other	Ichthyophthirius multifiliis the causative agent of white spot disease is associated with high mortality morbidity and significant economic losses in both the aquaculture and ornamental fish industries. I. multifiliis exhibits low host specificity infecting nearly all freshwater fish species with severe cases reported in rainbow trout Oncorhynchus mykiss common carp Cyprinus carpio and channel catfish Ictalurus punctatus. In contrast zebrafish Danio rerio display a high level of natural resistance to the parasite. The immunological mechanisms underlying this resistance are not fully understood though it has been suggested that early immune responses during infection may influence disease severity. Understanding these early responses and the mechanisms of natural resistance could aid in mitigating the disease and provide insights into protective immunity. The aim of this study was to investigate the early immunological response to I. multifiliis infection in naturally resistant zebrafish and susceptible rainbow trout using transcriptomics. Zebrafish and rainbow trout were infected with I. multifiliis and gill samples were collected at 2 24 48 and 72 hours post infection hpi for transcriptomic analysis. Results showed that zebrafish mounted a strong immune response peaking at 24 hpi with 1 231 differentially expressed DE genes before returning to normal levels. In contrast rainbow trout exhibited a much weaker response with only 28 DE genes at 24 hpi and the response normalized by 72 hpi. In zebrafish DE genes were associated with six immune related pathways however all DE genes were significantly downregulated suggesting that the zebrafish may have cleared the infection early negating the need for further immune activation. This was confirmed by a decrease in the number of transcripts mapping to the I. multifiliis genome in zebrafish however in rainbow trout the number of mapping transcripts increased over time indicating disease progression. Several cytokines related to cellular immune responses such as Cxcl8a Cxcl13 and Cxcl11 were upregulated highlighting the role of immune cells in combating I. multifiliis. Overall this study supports the idea that early immune responses are critical in determining the severity of I. multifiliis infection.	ENA FIRST PUBLIC:2024 11 01\|ENA LAST UPDATE:2024 11 01		ZF Inf 48h F2 T1	ZF Inf 48h F2 T1	SAMEA116144999	CEH,Center for Evolutionary Hologenomics	ENA first public:2024 12 19\|INSDC center name:CEH Center for Evolutionary Hologenomics\|INSDC status:public\|Submitter Id:ZF Inf 48h F2 T1\|collection date:2021 09 20\|common name:zebrafish\|geographic location country and/or sea:Denmark\|hpi:48\|sample name:ZF Inf 48h F2 T1\|scientific name:Danio rerio\|status:infected\|tissue type:gill									Illumina NovaSeq 6000 paired end sequencing	ena EXPERIMENT TAB 19 12 2024 10:07:07:239 27839	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP165174	Illumina NovaSeq 6000 paired end sequencing	ENA FIRST PUBLIC:2024 12 19\|ENA LAST UPDATE:2024 12 19	ZF_Inf_48h_F2_T1.pair1.truncated ZF_Inf_48h_F2_T1.pair2.truncated	fastq fastq	10400268770.0	34736762.0	ena RUN TAB 19 12 2024 10:07:07:239 27840	0:149.70 1:149.70	A:2850649951;C:2367895411;G:2362604415;T:2819029152;N:89841	149	149			2850649951	2367895411	2362604415	2819029152	89841	ERX13488950	ERS21188940	ERA31046805	ceh,center for evolutionary hologenomics\|European Nucleotide Archive	ceh,center for evolutionary hologenomics												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Denmark	2024-11-01	Undetermined	Undetermined	Gill	Respiratory System