School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
Fish Shellfish Immunol. 2020 Nov;106:1078-1086. doi: 10.1016/j.fsi.2020.09.015. Epub 2020 Sep 16.
Lacking full-length transcriptome for black rockfish (Sebastes schlegelii) limits novel gene discoveries and gene structures analysis. Therefore, we constructed the full-length transcriptome of black rockfish using Single-Molecule Real-Time Sequencing technology. Totally, we produced 21.73 Gb raw reads containing 298,904 circular consensus sequence (CCS) reads. Full-length (FL) and Non-full-length (NFL) isoforms were obtained based on the presence of 5' and 3' primers as well as poly (A) tails. The results showed 70.71% reads were identified as FL isoforms. Moreover, the average length of these PacBio isoforms is 2,632 bp, which is much longer than the length of the unigenes with the average length of 589 bp which generated from Illumina platform. Meanwhile, we identified 43,068 non-redundant transcripts, 12,485 alternative splicing (AS), 6,320 polyadenylation (APA) and 499 gene fusions as well as numerous long non-coding RNAs based on mapped FL isoforms. In addition, we identified 147 and 528 immune-related genes from novel genes and unmapped transcripts. The provided dataset can be utilized to discover novel genes and construct a comprehensive transcript dataset for black rockfish.
缺乏完整的黑鲷（Sebastes schlegelii）转录组限制了新基因的发现和基因结构分析。因此，我们使用单分子实时测序技术构建了黑鲷的全长转录组。总共产生了 21.73Gb 的原始读数，其中包含 298904 条圆形一致序列（CCS）读数。根据 5'和 3'引物以及聚（A）尾巴的存在，获得了全长（FL）和非全长（NFL）异构体。结果表明，70.71%的读数被鉴定为 FL 异构体。此外，这些 PacBio 异构体的平均长度为 2632bp，比 Illumina 平台生成的平均长度为 589bp 的 unigenes长得多。同时，我们根据映射的 FL 异构体鉴定了 43068 个非冗余转录本、12485 个可变剪接（AS）、6320 个多聚腺苷酸化（APA）和 499 个基因融合以及大量长非编码 RNA。此外，我们从新基因和未映射的转录本中鉴定了 147 个和 528 个免疫相关基因。提供的数据集可用于发现新基因并构建黑鲷的综合转录组数据集。
