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Discovery and annotation of novel microRNAs in the porcine genome by using a semi-supervised transductive learning approach

机译：利用半监控转膜学习方法发现和注释猪基因组中的新微大研讨会

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Despite the broad variety of available microRNA (miRNA) prediction tools, their application to the discovery and annotation of novel miRNA genes in domestic species is still limited. In this study we designed a comprehensive pipeline (eMIRNA) for miRNA identification in the yet poorly annotated porcine genome and demonstrated the usefulness of implementing a motif search positional refinement strategy for the accurate determination of precursor miRNA boundaries. The small RNA fraction from gluteus medius skeletal muscle of 48 Duroc gilts was sequenced and used for the prediction of novel miRNA loci. Additionally, we selected the human miRNA annotation for a homology-based search of porcine miRNAs with orthologous genes in the human genome. A total of 20 novel expressed miRNAs were identified in the porcine muscle transcriptome and 27 additional novel porcine miRNAs were also detected by homology-based search using the human miRNA annotation. The existence of three selected novel miRNAs (ssc-miR-483, ssc-miR484 and ssc-miR-200a) was further confirmed by reverse transcription quantitative real-time PCR analyses in the muscle and liver tissues of G?ttingen minipigs. In summary, the eMIRNA pipeline presented in the current work allowed us to expand the catalogue of porcine miRNAs and showed better performance than other commonly used miRNA prediction approaches. More importantly, the flexibility of our pipeline makes possible its application in other yet poorly annotated non-model species.
机译：尽管各种各样的可用MicroRNA（miRNA）预测工具，但它们在国内物种中的新型miRNA基因的发现和注释的应用仍然有限。在这项研究中，我们设计了一种综合管线（EMIRNA）在尚未注释的猪基因组中进行miRNA鉴定，并展示了实施MOTIF搜索位置改进策略的有用性，以准确测定前体miRNA边界。测序来自Gluteus medius骨骼肌的小RNA部分，并用于预测新的miRNA基因座。另外，我们选择了人类miRNA注释，用于在人类基因组中具有正非基因的猪miRNA的基于猪MiRNA的基于猪miRNA的诠释。在猪肌肉转录组中鉴定了总共20种新型表达的miRNA，并且还通过使用人miRNA注释通过基于同源的搜索检测到额外的新型猪miRNA。通过逆转录的定量实时PCR分析，进一步证实了G-Tdingen Minipigs的肌肉和肝组织中的逆转录定量实时PCR进一步证实了三种选定的新型miRNA（SSC-MIR-483，SSC-MIR484和SSC-MIR-200a）。总之，目前工作中提供的EMIRNA管道允许我们扩展猪MiRNA的目录，并且表现出比其他常用的miRNA预测方法更好的性能。更重要的是，我们的管道的灵活性使其应用于其他尚未注释的非模型物种。

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