TY - JOUR
T1 - Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq
AU - Dettleff, Phillip
AU - Hormazabal, Elizabeth
AU - Aedo, Jorge
AU - Fuentes, Marcia
AU - Meneses, Claudio
AU - Molina, Alfredo
AU - Valdes, Juan Antonio
N1 - Funding Information:
This study was supported by CONICYT/FONDAP/15110027 awarded to Juan Antonio Valdés and Alfredo Molina and CONICYT FONDECYT Postdoctorado 3180283 awarded to Phillip Dettleff.
PY - 2020/2/1
Y1 - 2020/2/1
N2 - The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.
AB - The red cusk-eel (Genypterus chilensis) is a native species with strong potential to support Chilean aquaculture diversification. Under commercial conditions, fish are exposed to several stressors. To date, little is known about the mechanism involved in the stress response of red cusk-eel, and there is no information related to the regulation mediated by long noncoding RNAs (lncRNAs). The objective of this work was to identify for the first time the lncRNAs in the transcriptome of G. chilensis and to evaluate the differential expression levels of lncRNAs in the liver, head kidney, and skeletal muscle in response to handling stress. We used previously published transcriptome data to identify the lncRNAs by applying a series of filters based on annotation information in several databases to discard coding sequences. We identified a total of 14,614 putative lncRNAs in the transcriptome of red cusk-eel, providing a useful lncRNA reference resource to be used in future studies. We evaluated their differential expression in response to handling stress in the liver, head kidney, and skeletal muscle, identifying 112, 323, and 108 differentially expressed lncRNAs, respectively. The results suggest that handling stress in red cusk-eel generate an altered metabolic status in liver, altered immune response in head kidney, and skeletal muscle atrophy through an important coding and noncoding gene network. This is the first study that identifies lncRNAs in Genypterus genus and that evaluates the relation between handling stress and lncRNAs in teleost fish, thereby providing valuable information regarding noncoding responses to stress in Genypterus species.
KW - Genypterus chilensis
KW - Long noncoding RNA
KW - Red cusk-eel
KW - RNA-seq
KW - Stress response
UR - http://www.scopus.com/inward/record.url?scp=85075399446&partnerID=8YFLogxK
U2 - 10.1007/s10126-019-09934-6
DO - 10.1007/s10126-019-09934-6
M3 - Article
AN - SCOPUS:85075399446
VL - 22
SP - 94
EP - 108
JO - Molecular Marine Biology and Biotechnology
JF - Molecular Marine Biology and Biotechnology
SN - 1436-2228
IS - 1
ER -