Prasad Priti, Khatoon Uzma, Verma Rishi Kumar, Aalam Shahre, Kumar Ajay, Mohapatra Debashish, Bhattacharya Parthasarthi, Bag Sumit K, Sawant Samir V
Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
Front Plant Sci. 2022 Feb 24;13:811655. doi: 10.3389/fpls.2022.811655. eCollection 2022.
Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the "CottonExpress-omics" database.
棉纤维发育仍是一个理解纤维起始和发育的有趣问题。在不同的纤维发育阶段，许多基因改变其表达模式，并在纤维品质和产量中发挥关键作用。最近，针对纤维的转录调控进行了大量研究，原始数据已存入公共数据库以供全面综合分析。在此，我们使用统一的映射策略重新映射了超过380个棉花RNAseq数据，该策略覆盖基因组约400倍的范围。我们确定了与纤维细胞起始、起始、伸长和次生细胞壁（SCW）合成相关的阶段特异性特征，以及它们在纤维发育中特定调控的假定顺式调控元件。我们还挖掘了在棉花纤维进化和驯化过程中被正向选择的特异性表达转录本（EETs）。此外，通过nCounter分析在100个棉花基因型中验证了EETs的表达，并将其与不同的纤维相关性状相关联。因此，我们的数据挖掘研究揭示了与棉花纤维发育和改良相关的几个重要特征，这些特征整合在“CottonExpress-组学”数据库中。
