Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus

Abstract

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.

The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (Sander lucioperca)

“…Some mature miRNAs, like slu-mir-21-1-2-5p, slu-mir-22ab-3p, and slu-mir-26a-1-3-5p, were ubiquitously enriched throughout the stages. These mature miRNAs also had similar high abundances in all organs and developmental stages in other teleost fish [ 14 , 22 ]. Together, this indicates housekeeping functions that are conserved across species.…”

“…In line with this is the finding that they regulate hox genes in Nile tilapia embryonic development [ 56 ] and also mediate cell proliferation and differentiation [ 57 ]. The mature members slu-mir-9-1-4-5p and slu-mir-7ab-5p have been reported as highly abundant in early developmental stages, as well as in the brain [ 14 , 22 , 58 , 59 , 60 , 61 ]. It is likely that their high relative abundance in early developmental groups in pikeperch reflect similar functions.…”

“…Data on the miRNA repertoire in teleosts are still limited, with only 16 out of the over 26,000 teleost fish species being present in miRBase (22 October 2023; ). Nevertheless, research on teleostean miRNAs has increased significantly (reviewed in [ 9 , 10 , 11 ]), as has research on fish models including zebrafish ( Danio rerio ) [ 12 , 13 ] and economically relevant species like Atlantic salmon ( Salmo salar ) [ 14 , 15 ], rainbow trout ( Oncorhynchus mykiss ) [ 16 , 17 ], Nile tilapia ( Oreochromis niloticus ) [ 18 , 19 ], Atlantic cod ( Gadus morhua ) [ 20 , 21 ], lumpfish ( Cyclopterus lumpus ) [ 22 ], and channel catfish ( Ictalurus punctatus ) [ 23 , 24 ]. In addition, the recently developed FishmiRNA database also provides miRNAs for black bullhead ( Ameiurus melas ), Japanese medaka ( Oryzias latipes ), molly ( Poecilia mexicana ), European perch ( Perca flavescens ), stickleback (Gasterosteus aculeatus ), and blackfin icefish ( Chaenocephalus aceratus ) [ 25 ].…”

Transcriptome and Genome Analyses Applied to Aquaculture Research

“…But not only does the expression pattern of the protein-coding genes changes during development, the expression of ncRNAs, as regulators of the gene expression, is also fine-tuned during development. To obtain the complete miRNAome of lumpfish ( Cyclopterus lumpus ), Chakraborty et al [ 24 ] conducted miRNA analysis of different organs from adult individuals and entire embryos and larvae. They obtained 443 unique mature miRNAs from 391 conserved and eight novel miRNA genes, which represent an essential reference for future expression analyses.…”

“…They obtained 443 unique mature miRNAs from 391 conserved and eight novel miRNA genes, which represent an essential reference for future expression analyses. Additionally, the expression patterns of specific conserved miRNAs in particular tissues and developmental stages indicated that they are involved in organ- and developmental stage-specific functions reported in other teleost [ 24 ]. To obtain as most complete as possible a first transcriptome of edible red sea urchin, Loxechinus albus was the objective of Antiqueo et al [ 25 ].…”