Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica
Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica
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DOI：
10.1007/s10126-022-10163-7
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发表时间：
2022-09
影响因子：
3
通讯作者：
Yuan Zhang;Fangrui Lou;Jianwei Chen;Zhiqiang Han;Tianyan Yang;T. Gao;N. Song
中科院分区：
文献类型：
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作者：
Yuan Zhang;Fangrui Lou;Jianwei Chen;Zhiqiang Han;Tianyan Yang;T. Gao;N. Song
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 ofS. sinicausing 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 ofS. 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 ofS. sinicawould provide a precious resource for characterizing the transcriptome ofS. sinicaand for the further study of gene function and regulatory mechanism of this species.
