Integrative microRNAome analysis of skeletal muscle of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu), and the hybrid tambacu, based on nextgeneration sequencing data
- Conclusions: Our global miRNA analysis provided interesting DE miRNAs in the skeletal muscle of pacu, tambaqui, and the hybrid tambacu. - In addition, in the hybrid tambacu, we identified some miRNAs controlling important molecular muscle markers that could be relevant for the farming maximization.. - Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are fish species that have widely accepted in the consumer market. - The skeletal muscle is directly involved in the growth of the fish, corresponding to about 35–60% of the body weight of the animal [8]. - Some miRNAs are known to be specifically or highly expressed in the cardiac and/or skeletal muscles and have been dubbed “myo-miRs” [14]. - A relative high number of DE miRNAs are ob- served in the data. - A similar characteristic was observed in the down-regulated miRNAs, where miR- 199-3-3p appears downregulated in TC when compared with both PC and TQ. - These miRNAs are considered as TC-exclusive (in terms of expression levels), as they ap- pear to be up- or down-regulated only in the hybrid compared to the parental species, but not between par- ental species (Fig. - Also, we detected some up- or down-regulated miRNAs only in the hybrid, representing a specific characteristic of this genotype.. - In the search for target genes involved in DE miRNAs expression, we searched for experimentally validated tar- gets using miRTarBase dataset version 7 [16]. - In the present study, global analysis of miRNAs in the three genotypes identified a small number of differen- tially expressed miRNAs considering the comparison be- tween the genotypes pairs. - TC vs. - TQ (miR-187, miR-18a, miR-190a, miR-206-3p, miR-221-3p, miR-27b-3p, miR- 29a, miR-363-3p, and miR-727-5p), some of which were exclusive in the comparison between PC vs. - characteristic of being inherited specifically of one geno- type, and also, there were some miRNAs that appeared to be up- or down-regulated only in the hybrid (miR- 10a-5p, miR-144-3p, and miR-199-3-3p). - These miRNAs presented (up or downregulated) behavior, exclusively in the hybrid, not differentially expressed between the par- ental genotypes.. - dre-miR-216b.path E+ 07. - dre-miR-216a.path E+ 07. - dre-miR-2188-5p.path . - dre-miR-451.path . - dre-miR-144-3p.path . - dre-miR-10a-5p.path . - dre-miR-1388-5p.path . - dre-miR-210-5p.path . - dre-miR-22a-5p.path . - dre-miR-138-5p.path . - dre-miR-199-3-3p.path . - dre-miR-375.path . - dre-miR-132-3p.path . - The more enriched genes in the signal- ing pathway involved in these processes were alas2, jun, and lmo2.. - miR-206-3p, identified in the present study, was differen- tially expressed in the comparison pair TC vs. - As jun and vegfa genes are targets of miR-206-3p and, as this miRNA was observed to be differentially expressed in the comparison pair TC vs. - involved in the maintenance of blood irrigation that, in turn, controls the oxygen rates in the tissues.. - The miRNA involved in the control of the alas2 and lmo2 genes was miR-144-3p. - This miRNA appeared up- regulated in the comparison pairs TC vs. - TQ and did not appear in the comparison between the parental genotypes PC vs. - dre-miR-499-5p.path . - dre-miR-499-3p.path . - dre-miR-122.path . - dre-miR-7a.path . - dre-miR-184.path . - dre-miR-206-3p.path . - dre-miR-27d.path E+ 09. - dre-miR-192.path . - dre-miR-27b-3p.path . - dre-miR-363-3p.path . - dre-miR-212-5p.path . - dre-miR-187.path . - dre-miR-18a.path . - dre-miR-29a.path . - dre-miR-221-3p.path E+ 06. - dre-miR-190a.path . - dre-miR-727-5p.path . - dre-miR-19d-3p.path . - dre-miR-223.path . - dre-miR-155.path . - We believe that this is an important characteristic that probably could provide, for the hybrid tambacu, more resistance to environments with lower oxygen content, once this miRNA was upregulated only in the hybrid, in the com- parison pairs TC vs. - DE only in the comparison pair TC vs. - macropomum and the hybrid tambacu, observed differences in the specificity and gene expres- sion levels in both the muscle and skin of the hybrid tambacu and the parental tambaqui [44]. - dre-miR-132-3p.path E+ 08. - dre-miR-489.path E+ 04. - dre-miR-146b.path . - dre-miR-26a-2-3p.path . - dre-miR-210-5p.path E+ 09. - dre-miR-216a.path . - dre-miR-2188-3p.path . - dre-miR-216b.path E+ 09. - demonstrated that in the muscle of tambaqui, up- regulated genes involved in muscle contraction, such as the myosin family, actin and myomesin, and catalytic protein genes. - 206-3p and miR-144-3p in the control of the robustness and faster growth of the hybrid tambacu [46].. - In addition, the most significant molecular function enriched by the targets of the up-regulated miRNAs in the tambacu muscle was transcriptional repressor activ- ity. - Using comparative global miRNA analysis in the hybrid tambacu and their parental genotypes Piaractus mesopota- micus and Colossoma macropomum, we demonstrated, for the first time, miRNAs differentially expressed in the skel- etal muscle of the genotype comparison pairs (TC vs. - The number marked in the overlapping areas shows the common DE miRNAs. - If a given miRNA appears up- or down-regulated only in the hybrid, it presents a hybrid-exclusive behavior. - If a given miRNA is up- or down-regulated in the one parental and in the hybrid, it presents a behavior inherited from that parental. - dre-miR-138-5p. - dre-miR-144-3p. - dre-miR-206-3p. - dre-miR-499-5p. - possible to locate the mature sequences in the precursor sequences and differentiate alignments between the 5′. - org/10.1186/s . - https://doi.org . - org/10.1023/A . - https://doi.org/10.1038/nrg3722.. - https://doi.org/10.1016/. - https://doi.org/10.1016/j.cell . - https://doi.org/10.1093/nar/gkx1067.. - Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. - Food restriction increase the expression of mTORC1 complex genes in the skeletal muscle of juvenile pacu (Piaractus mesopotamicus). - https://doi.org/10.1016/j.cellsig . - https://doi.org/10.1016/j.mvr . - A two-compartment model of VEGF distribution in the mouse. - https://doi.org/10.1152/physiolgenomics . - doi.org/10.1073/pnas . - doi.org/10.1093/emboj . - Transgenic rescue of erythroid 5-aminolevulinate synthase-deficient mice results in the formation of ring sideroblasts and siderocytes. - https://doi.org/10.1111/j x.. - https://doi.org/10.1073/pnas.. - https://doi.org/10.1309/AJCP5FP3NAXAXRJE.. - https://doi.org/10.1007/s . - doi.org/10.1093/bioinformatics/bti310.. - https://doi.org/10.1093/bioinformatics/btt656.
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