Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus
MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lu...
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ftmdpi:oai:mdpi.com:/2079-7737/11/1/130/ 2023-08-20T04:05:20+02:00 Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus Setu Chakraborty Nardos T. Woldemariam Tina Visnovska Matthew L. Rise Danny Boyce Javier Santander Rune Andreassen agris 2022-01-13 application/pdf https://doi.org/10.3390/biology11010130 EN eng Multidisciplinary Digital Publishing Institute Genetics and Genomics https://dx.doi.org/10.3390/biology11010130 https://creativecommons.org/licenses/by/4.0/ Biology; Volume 11; Issue 1; Pages: 130 conserved miRNA high-throughput sequencing lumpfish novel miRNA RT-qPCR Text 2022 ftmdpi https://doi.org/10.3390/biology11010130 2023-08-01T03:49:52Z MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies. Text Atlantic salmon Salmo salar MDPI Open Access Publishing Biology 11 1 130 |
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MDPI Open Access Publishing |
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English |
topic |
conserved miRNA high-throughput sequencing lumpfish novel miRNA RT-qPCR |
spellingShingle |
conserved miRNA high-throughput sequencing lumpfish novel miRNA RT-qPCR Setu Chakraborty Nardos T. Woldemariam Tina Visnovska Matthew L. Rise Danny Boyce Javier Santander Rune Andreassen Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
topic_facet |
conserved miRNA high-throughput sequencing lumpfish novel miRNA RT-qPCR |
description |
MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies. |
format |
Text |
author |
Setu Chakraborty Nardos T. Woldemariam Tina Visnovska Matthew L. Rise Danny Boyce Javier Santander Rune Andreassen |
author_facet |
Setu Chakraborty Nardos T. Woldemariam Tina Visnovska Matthew L. Rise Danny Boyce Javier Santander Rune Andreassen |
author_sort |
Setu Chakraborty |
title |
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
title_short |
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
title_full |
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
title_fullStr |
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
title_full_unstemmed |
Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus |
title_sort |
characterization of mirnas in embryonic, larval, and adult lumpfish provides a reference mirnaome for cyclopterus lumpus |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2022 |
url |
https://doi.org/10.3390/biology11010130 |
op_coverage |
agris |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Biology; Volume 11; Issue 1; Pages: 130 |
op_relation |
Genetics and Genomics https://dx.doi.org/10.3390/biology11010130 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/biology11010130 |
container_title |
Biology |
container_volume |
11 |
container_issue |
1 |
container_start_page |
130 |
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1774715838692065280 |