PDF(Pubmed)
Abstract：
BACKGROUND: Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn.
RESULTS: A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified.
CONCLUSIONS: In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
RESULTS: A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified.
CONCLUSIONS: In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
摘要：
背景：东方河对虾（Macrobrachiumnipponense）是中国对虾养殖中最主要的物种之一，它是蛋白质的丰富来源，对人类生活质量有重大影响。因此，更完整、准确的基因模型注释对东方河虾的育种研究具有重要意义。
结果：使用PacBioSequel平台获得了东方河对虾肌肉的全长转录组。然后，对37.99Gb的亚读段进行了测序，包括584,498个环状共有序列，其中512,216个为全长非嵌合序列。在基于Illumina的长PacBio读数校正之后，鉴定了6,599个错误校正的同种型。转录组结构分析揭示了2,263和2,555个选择性剪接（AS）事件和选择性聚腺苷酸化（APA）位点，分别。总的来说,620个新基因（NGs），197个推定转录因子（TFs），并鉴定出291种新的长链非编码RNA(lncRNA)。
结论：总之，这项研究为这种对虾的转录组复杂性和多样性提供了新的见解，并为理解东方河虾的基因组结构和改进基因组草图注释提供了有价值的信息。
结果：使用PacBioSequel平台获得了东方河对虾肌肉的全长转录组。然后，对37.99Gb的亚读段进行了测序，包括584,498个环状共有序列，其中512,216个为全长非嵌合序列。在基于Illumina的长PacBio读数校正之后，鉴定了6,599个错误校正的同种型。转录组结构分析揭示了2,263和2,555个选择性剪接（AS）事件和选择性聚腺苷酸化（APA）位点，分别。总的来说,620个新基因（NGs），197个推定转录因子（TFs），并鉴定出291种新的长链非编码RNA(lncRNA)。
结论：总之，这项研究为这种对虾的转录组复杂性和多样性提供了新的见解，并为理解东方河虾的基因组结构和改进基因组草图注释提供了有价值的信息。
