Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii)

被引：23
作者：
Cao, Min [1 ]
Zhang, Min [1 ]
Yang, Ning [1 ]
Fu, Qiang [1 ]
Su, Baofeng [2 ]
Zhang, Xiaoyan [1 ]
Li, Qi [1 ]
Yan, Xu [3 ]
Thongda, Wilawan [4 ,5 ]
Li, Chao [1 ]
机构：
[1] Qingdao Agr Univ, Sch Marine Sci & Engn, Qingdao 266109, Peoples R China
[2] Auburn Univ, Sch Fisheries Aquaculture & Aquat Sci, Auburn, AL 36849 USA
[3] Qingdao Univ Sci & Technol, Coll Marine Sci & Biol Engn, Qingdao 266011, Peoples R China
[4] Mahidol Univ, Fac Sci, Ctr Excellence Shrimp Mol Biol & Biol CENTEX Shri, Rama VI Rd, Bangkok 10400, Thailand
[5] Natl Sci & Technol Dev Agcy NSTDA, Natl Ctr Genet Engn & Biotechnol BIOTEC, Pathum Thani 12120, Thailand
来源：
FISH & SHELLFISH IMMUNOLOGY | 2020年 / 106卷
关键词：
Black rockfish (Sebastes schlegelii); Single-Molecule Real-Time Sequencing; Full length transcriptome; Novel genes; Immune-related genes; JUVENILE ROCKFISH; BODY-COMPOSITION; PROTEIN; GROWTH; IDENTIFICATION;
D O I：
10.1016/j.fsi.2020.09.015
中图分类号：
S9 [水产、渔业];
学科分类号：
0908 ;
摘要：
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.
引用
收藏
页码：1078 / 1086
页数：9
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