Publication: Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii)
Issued Date
2020-11-01
Resource Type
ISSN
10959947
10504648
10504648
Other identifier(s)
2-s2.0-85091570823
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Mahidol University
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SCOPUS
Bibliographic Citation
Fish and Shellfish Immunology. Vol.106, (2020), 1078-1086
Suggested Citation
Min Cao, Min Zhang, Ning Yang, Qiang Fu, Baofeng Su, Xiaoyan Zhang, Qi Li, Xu Yan, Wilawan Thongda, Chao Li Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii). Fish and Shellfish Immunology. Vol.106, (2020), 1078-1086. doi:10.1016/j.fsi.2020.09.015 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/58889
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Title
Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii)
Abstract
© 2020 Elsevier Ltd 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.
