Abstract
BackgroundB chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood.ResultsWe identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B−) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples.ConclusionsThis study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.
Highlights
B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi
By combining the small RNA sequences (sRNAseq) with the availability of A. latifasciata genomic and mRNA transcriptomic data we described the miRNome of this cichlid species
The A. latifasciata miRNome A nonredundant dataset was constructed based on miRBase fish miRNAs to create a miRNA reference list
Summary
B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Recent advances in omics and big data technologies are revolutionizing the B biology field These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. A proto-B chromosome can emerge from chromosomal rearrangements, partial duplication of A chromosomes (normal chromosomes of the karyotype) or nonmeiotic disjunction [5] This new element increases its genomic content by insertion of A chromosome sequences copies, including various repetitive DNA classes [7,8,9], protein-coding genes [2, 10,11,12,13], pseudogenes [14], retrogenes [15], organellar DNA sequences [16] and noncoding sequences [17,18,19,20]. The characterization of the B genomic content and its effects using genomics and bioinformatics tools is a promising approach to understand this extra element and its relation to the host genome [21, 22]
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