Ali Ali, Thorgaard Gary H, Salem Mohamed
Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States.
School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States.
Front Genet. 2021 Jul 15;12:683408. doi: 10.3389/fgene.2021.683408. eCollection 2021.
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 () gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.
虹鳟是一种重要的模式生物，国际上已齐心协力对其转录组进行研究。为此，在过去十年中主要使用了短读长测序技术。然而，这些序列对于解析转录组的复杂性来说太短了。本研究报告了使用单分子长读长异构体测序（Iso-Seq）对虹鳟进行的首个全长转录组组装。采用了广泛的计算方法来优化和验证重建的转录组。该研究除了鉴定出1479个未映射到当前斯旺森参考基因组的异构体之外，还鉴定出10640个先前未注释的高可信度转录本。大多数鉴定出的长链非编码RNA（lncRNAs）是编码转录本的非编码变体。大多数基因具有多个转录异构体（平均每个基因座约3个异构体）。内含子保留（IR）和外显子跳跃（ES）占可变剪接（AS）事件的56%。Iso-Seq改善了参考基因组注释，从而能够鉴定与鱼类生长、肌肉积累、抗病性、应激反应和鱼类洄游相关的特征性可变剪接。例如，在易患细菌性冷水病（BCWD）的鱼类中存在某基因的外显子跳跃。此外，在五种应激条件下，脯氨酰4-羟化酶α-2亚基（）基因中存在一个共同调控的外显子。虹鳟中重建的基因模型及其转录后加工提供了宝贵的资源，可进一步用于未来的遗传学和基因组学研究。此外，该研究鉴定出了与经济上重要的表型相关的特征性转录事件，可应用于选择性育种。
