Fishery College, Ocean University of China, Qingdao, 266003, China.
School of Ocean, Yantai University, Yantai, 264005, China.
Mar Biotechnol (NY). 2022 Oct;24(5):1002-1013. doi: 10.1007/s10126-022-10163-7. Epub 2022 Sep 9.
As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.
作为一个新描述的沙塘鳢科物种，中国沙塘鳢（Sillago sinica）需要更好地了解基因注释信息。在本研究中，我们使用 PacBio 异构体测序 Iso-seq 报道了 S. sinica 的首个全长转录组数据，并描述了转录组结构分析。通过单分子实时 (SMRT) 测序获得了 454,979 条高质量全长转录本，并用 Illumina 测序数据进行了校正。之后，将其映射到中国沙塘鳢参考基因组后，生成了 66,948 条非冗余全长转录本，其中包括 49 个融合异构体和 9,250 个新异构体。通过 Nr、Nt、SwissProt、Pfam、KOG、GO 和 KEGG 数据库之一成功注释了 63,459 个异构体。此外，鉴定了 30,987 个可变多聚腺苷酸化 (APA) 位点、451,867 个可变剪接 (AS) 事件、21,928 个长非编码 RNA (lncRNA) 和 12,911 个转录因子 (TF)。中国沙塘鳢的全长转录本将为研究中国沙塘鳢的转录组以及进一步研究该物种的基因功能和调控机制提供宝贵的资源。
