PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense
文献类型： 外文期刊
作者： Mou, Cheng-Yan 1 ; Li, Qiang 1 ; Huang, Zhi-Peng 1 ; Ke, Hong-Yu 1 ; Zhao, Han 1 ; Zhao, Zhong-Meng 1 ; Duan, Yuan-Liang 1 ; Li, Hua-Dong 1 ; Xiao, Yu 2 ; Qian, Zhou-Ming 3 ; Du, Jun 1 ; Zhou, Jian 1 ; Zhang, Lu 1 ;
作者机构： 1.Sichuan Acad Agr Sci, Fisheries Inst, Chengdu 611731, Sichuan, Peoples R China
2.Sichuan Acad Agr Sci, Chengdu 610066, Sichuan, Peoples R China
3.Chengdu Eaters Agr Grp Co Ltd, Chengdu 610000, Sichuan, Peoples R China
关键词： Long non-coding RNA; Novel genes; Alternative splicing; Alternative polyadenylation; SMRT sequencing; Oriental river prawn
期刊名称：BMC GENOMICS （ 影响因子：4.4； 五年影响因子：4.7 ）
ISSN： 1471-2164
年卷期： 2023 年 24 卷 1 期
页码：
收录情况： SCI
摘要： BackgroundOriental 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.ResultsA 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.ConclusionsIn 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.
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