一种用于非模式植物物种基因发现与验证的网络驱动流程。

A network-enabled pipeline for gene discovery and validation in non-model plant species.

作者信息

Ko Dae Kwan, Brandizzi Federica

机构信息

MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.

出版信息

Cell Rep Methods. 2025 Jan 27;5(1):100963. doi: 10.1016/j.crmeth.2024.100963.

DOI:10.1016/j.crmeth.2024.100963

PMID:39874949

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11840947/

Abstract

Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 (CSLF6), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum. Our analyses uncover regulators of CSLF6 and also shed light on the evolutionary conservation or divergence of gene regulatory elements among grass species. These results highlight NEEDLE's capability to provide biologically relevant TF predictions and demonstrate its value for non-model plant species with dynamic transcriptome datasets.

摘要

由于多组学资源有限，识别非模式作物物种中重要基因的关键调控因子具有挑战性。为了解决这一问题，我们引入了基于网络的基因发现管道NEEDLE，这是一个用户友好的工具，它系统地生成共表达基因网络模块，测量基因连通性，并建立网络层次结构，以从动态转录组数据集中找出关键的转录调控因子。在用两个独立数据集验证其准确性后，我们应用NEEDLE来鉴定调节纤维素合酶样F6（CSLF6）表达的转录因子（TF），CSLF6是一种关键的细胞壁生物合成基因，存在于短柄草和高粱中。我们的分析揭示了CSLF6的调控因子，也阐明了禾本科物种间基因调控元件的进化保守性或差异性。这些结果突出了NEEDLE提供生物学相关TF预测的能力，并证明了其对于具有动态转录组数据集的非模式植物物种的价值。