利用 RNA-Seq 分析环孢素 A/DIAGEOTROPICA（DGT）在番茄根发育中影响的基因。

RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development.

机构信息

Department of Botany and Plant Pathology, Oregon State University, 2701 SW Campus Way, Corvallis, Oregon, 97331, USA.

Biochemistry and Molecular Biology Program, Oregon State University, 2701 SW Campus Way, Corvallis, Oregon, 97331, USA.

出版信息

F1000Res. 2020 Sep 28;9:1175. doi: 10.12688/f1000research.25750.1. eCollection 2020.

DOI:10.12688/f1000research.25750.1

PMID:33123350

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7570327/

Abstract

Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype ('Ailsa Craig') and tissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.

摘要

亲环蛋白 A/DIAGEOTROPICA（DGT）与番茄中生长素调控的发育有关，似乎影响多种发育途径。DGT 功能丧失导致表型多效性，在根中最为明显，包括根变短，没有侧枝。在这里，我们展示了一个 RNA-Seq 数据集，比较了野生型（“Ailsa Craig”）和番茄根尖三个空间分离的发育阶段的组织的基因表达谱，每个组织和基因型有三个重复。我们还鉴定了差异表达基因，对每个基因型和组织中受影响的基因进行了初步比较，并提供了用于分析数据的流程。对该数据集的进一步分析可用于深入了解 DGT 对番茄各种根发育途径的影响。