Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures

Common wheat is allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3’ RNA-seq, is a technology efficient at obtaining homoeolog-distinguished transcriptomes. Here we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia. Roots and seedlings were similar to each other in transcriptome profiles, but they were different from the leaves. We then asked how three homoeologous genes from different subgenomes (i.e., triads) show different levels of expression. Specifically, we examined the effects of subgenomes, lines, and their interaction on the expression levels of each homoeolog triad, separately in each tissue. Of the 19,805 homoeolog triads, 51–55% showed significant effect of subgenome, suggesting cis-regulation, whereas 24–30% showed significant effect line, suggesting trans-regulation. We also found that 7.7–9.0% triads showed significant e..., This study obtained transcriptome data from seedlings, second leaves, and root tips of four replications of 25 NAM parental lines using Lasy-Seq. , , # Dataset: Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures

[https://doi.org/10.5061/dryad.fqz612jzq](https://doi.org/10.5061/dryad.fqz612jzq)

This study obtained transcriptome data from seedlings, second leaves, and root tips of four replications of 25 NAM parental lines using Lasy-Seq. Roots and seedlings were similar transcriptome profiles to each other and different from leaves. We determined the effects of subgenomes, lines, and their interactions by leaves, roots and seedlings on expression levels for each homoeolog triads. Of the 19,805 homoeolog triads, the percentages of homoeolog triads with significant subgenome, line and interaction effects were 50.9–55.4%, 24.2–29.5% and 7.7–9.0%, respectively. GO term enrichment analysis showed that GO terms related to each tissue type function were enriched in expressed genes in leaves and roots.

## Description of the data and file structure

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普通小麦为异源六倍体，难以获取区分同源染色体基因（homoeolog）的转录组数据。Lasy-Seq是一种3′ RNA-seq技术，能高效获得区分同源染色体基因的转录组。本研究应用Lasy-Seq技术，对25份主要来自东亚的普通小麦品系的幼苗、第二叶及根尖进行转录组数据采集。根与幼苗的转录组谱相似，但与叶片存在差异；随后探究了来自不同亚基因组三个同源基因（即三联体，triads）表达水平差异的机制。具体而言，我们在各组织中分别分析亚基因组、品系及其交互作用对每个同源基因三联体表达水平的影响。在19805个同源基因三联体中，51%~55%表现出显著亚基因组效应（提示顺式调控，cis-regulation），24%~30%表现出显著品系效应（提示反式调控，trans-regulation）；还发现7.7%~9.0%的三联体表现出显著的……本研究通过Lasy-Seq技术获取25份NAM亲本系四个重复样本的幼苗、第二叶及根尖转录组数据。

# 数据集：基于亚基因组信息的25份普通小麦材料转录组统计建模揭示顺式与反式调控架构

[https://doi.org/10.5061/dryad.fqz612jzq](https://doi.org/10.5061/dryad.fqz612jzq)

本研究通过Lasy-Seq技术获取25份NAM亲本系四个重复样本的幼苗、第二叶及根尖转录组数据。根与幼苗转录组谱相似，且与叶片不同。我们针对叶片、根和幼苗分别分析亚基因组、品系及其交互作用对每个同源基因三联体表达水平的影响。在19805个同源基因三联体中，表现出显著亚基因组效应、品系效应及交互作用效应的比例分别为50.9%~55.4%、24.2%~29.5%和7.7%~9.0%。基因本体（GO）术语富集分析显示，与各组织功能相关的GO术语在叶片和根的表达基因中富集。

## 数据及文件结构描述

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