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

Ko, Dae Kwan; Brandizzi, Federica

doi:10.1016/j.crmeth.2024.100963

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

Journal Article · 27 January 2025 · Cell Reports. Methods

DOI: https://doi.org/10.1016/j.crmeth.2024.100963 · OSTI ID:2507135

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Michigan State Univ., East Lansing, MI (United States)

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.

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Research Organization:: Chicago Office, Argonne, IL (United States); Michigan State Univ., East Lansing, MI (United States); Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory

Sponsoring Organization:: Great Lakes Bioenergy Research Center; National Institute of General Medical Sciences; USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FG02-91ER20021; SC0018409

OSTI ID:: 2507135

Journal Information:: Cell Reports. Methods, Journal Name: Cell Reports. Methods Journal Issue: 1 Vol. 5; ISSN 2667-2375

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
crop genomics
gene discovery
gene regulatory networks
network modeling
transcriptional regulation
transcriptomics

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

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