当前位置: X-MOL 学术Fish Shellfish Immun. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii).
Fish & Shellfish Immunology ( IF 4.7 ) Pub Date : 2020-09-16 , DOI: 10.1016/j.fsi.2020.09.015
Min Cao 1 , Min Zhang 1 , Ning Yang 1 , Qiang Fu 1 , Baofeng Su 2 , Xiaoyan Zhang 1 , Qi Li 1 , Xu Yan 3 , Wilawan Thongda 4 , Chao Li 1
Affiliation  

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 2632 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), 6320 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.



中文翻译:

全长转录组分析揭示了黑石鱼(Sebastes schlegelii)中新的免疫相关基因。

黑色石鱼(Sebastes schlegelii)缺少全长转录组)限制了新的基因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色岩鱼的全长转录组。总的来说,我们产生了21.73 Gb原始读取,其中包含298,904个环状共有序列(CCS)读取。基于5'和3'引物以及poly(A)尾巴的存在,获得了全长(FL)和非全长(NFL)同工型。结果显示70.71%的读数被鉴定为FL同工型。此外,这些PacBio同工型的平均长度为2632 bp,比Illumina平台产生的单基因的平均长度589 bp长得多。同时,我们确定了43,068个非冗余成绩单,12,485个选择性剪​​接(AS),6320聚腺苷酸化(APA)和499基因融合,以及许多基于定位FL同种型的长非编码RNA。此外,我们从新基因和未映射的转录本中鉴定了147和528个与免疫相关的基因。提供的数据集可用于发现新基因并构建黑石鱼的完整转录本数据集。

更新日期:2020-09-16
down
wechat
bug