Alexandre Santos Simeone

Os RNAs longos não-codificadores (lncRNAs) destacam-se como importantes moduladores da expressão gênica, desempenhando papéis críticos na regulação epigenética, controle transcricional e regulação pós-transcricional. Suas interações complexas com proteínas, DNA e outros RNAs possibilitam uma modulação gênica multifacetada, essencial tanto para a homeostase celular quanto para a progressão de diversas patologias, incluindo câncer. Avanços em ferramentas computacionais, especialmente técnicas de machine learning e deep learning, aprimoram a identificação e a predição de lncRNAs, permitindo a análise de grandes conjuntos de dados transcriptômicos e a integração de características moleculares e homologia genética. Além disso, os lncRNAs apresentam potencial como biomarcadores diagnósticos e alvos terapêuticos, oferecendo perspectivas promissoras para o diagnóstico precoce e intervenções terapêuticas. Entretanto, persistem desafios relacionados à validação experimental e ao entendimento detalhado dos mecanismos moleculares dos lncRNAs. Esta revisão examina as funções moleculares e implicações clínicas dos lncRNAs, abordando ainda os avanços nas ferramentas bioinformáticas para sua predição e aplicações na medicina.

Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.

Cobia ( Rachycentron canadum ) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyzes with Danio rerio , Lates calcarifer , Seriola lalandi dorsalis , Seriola dumerili or Echeneis naucrates . Finally, we identified 7,894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.