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Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton
Journal of Advanced Research ( IF 10.7 ) Pub Date : 2023-05-18 , DOI: 10.1016/j.jare.2023.05.004
Ghulam Qanmber 1 , Qi You 2 , Zhaoen Yang 1 , Liqiang Fan 3 , Zhibin Zhang 3 , Mao Chai 3 , Baibai Gao 4 , Fuguang Li 1 , Zuoren Yang 1
Affiliation  

The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton () remains unexplored. We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of , a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.

中文翻译:

转录和平移景观微调基因组注释并探索棉花的翻译控制

介绍

全基因组测序和泛基因组学中基因间区域注释的不可用性阻碍了加强作物改良的努力。

目标

尽管研究取得了进展,但转录后调控对棉花 ( G. hirsutum )纤维生长不同阶段纤维发育和翻译组分析的影响仍未得到探索。

方法

我们结合使用参考引导的从头转录组组装和核糖体分析技术来揭示陆地棉八种不同组织中翻译控制的隐藏机制。

结果

我们的研究确定了三核苷酸周期的 P 位点分布和 27 个核苷酸的主要核糖体足迹。具体而言,我们检测到 1,589 个小开放阅读框 (sORF),包括 1,376 个上游 ORF (uORF) 和 213 个下游 ORF (dORF),以及 552 个具有潜在编码功能的长链非编码 RNA (lncRNA),可微调棉花基因组注释。此外,我们已经鉴定出具有高翻译效率 (TE) 的新基因和 lncRNA,同时发现 sORF 在纤维伸长过程中影响 mRNA 转录水平。RNA 测序 (RNA-seq) 和核糖体测序 (Ribo-seq) 分析之间相关性和协同倍数变化的高度一致性证实了这些发现的可靠性。此外,正常纤维ZM24和短纤维的综合组学分析pag1棉花突变体揭示了几个差异表达基因 (DEG),以及与 sORF(uORF 和 dORF)相关的纤维特异性表达(高/低)基因。GhKCS6的过表达和敲低进一步支持了这些发现, GhKCS6是一种与棉花中的 sORF 相关的基因,并证明了在转录和转录后水平上控制纤维伸长的机制的潜在调节。

结论

参考指导的转录组组装和新转录本的鉴定微调了棉花基因组的注释并预测了纤维发育的前景。我们的方法提供了一种基于多组学的高通量方法,用于发现农作物中未注释的 ORF、隐藏的翻译控制和复杂的调控机制。

更新日期:2023-05-18
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