State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
BMC Genomics. 2022 May 10;23(1):357. doi: 10.1186/s12864-022-08551-3.
The DoG (Delay of Germination1) family plays a key regulatory role in seed dormancy and germination. However, to date, there is no complete genomic overview of the DoG gene family of any economically valuable crop, including moso bamboo (Phyllostachys edulis), and no studies have been conducted to characterize its expression profile. To identify the DoG gene members of moso bamboo (PeDoG) and to investigate their family structural features and tissue expression profile characteristics, a study was conducted. Based on the whole genome and differential transcriptome data, in this investigation, we have scrutinized the physicochemical properties, gene structure, cis-acting elements, phylogenetic relationships, conserved structural (CS) domains, CS motifs and expression patterns of the PeDoG1 family of moso bamboo.
The DoG family genes of moso bamboo were found distributed across 16 chromosomal scaffolds with 24 members. All members were found to carry DoG1 structural domains, while 23 members additionally possessed basic leucine zipper (bZIP) structural domains. We could divide the PeDoG genes into three subfamilies based on phylogenetic relationships. Covariance analysis revealed that tandem duplication was the main driver of amplification of the PeDoG genes. The upstream promoter of these genes containing several cis-acting elements indicates a plausible role in abiotic stress and hormone induction. Gene expression pattern according to transcriptome data revealed participation of the PeDoG genes in tissue and organ development. Analysis using Short Time-series Expression Miner (STEM) tool revealed that the PeDoG gene family is also associated with rapid early shoot growth. Gene ontology (GO) and KEGG analyses showed a dual role of the PeDoG genes. We found that PeDoGs has a possible role as bZIP transcription factors by regulating Polar like1 (PL1) gene expression, and thereby playing a disease response role in moso bamboo. Quantitative gene expression of the PeDoG genes revealed that they were abundantly expressed in roots and leaves, and could be induced in response to gibberellin (GA).
In this study, we found that the PeDoG genes are involved in a wide range of activities such as growth and development, stress response and transcription. This forms the first report of PeDoG genes and their potential roles in moso bamboo.
DOG（延迟萌发 1）家族在种子休眠和萌发中起着关键的调节作用。然而，迄今为止，包括毛竹（Phyllostachys edulis）在内的任何有经济价值的作物的 DOG 基因家族都没有完整的基因组概述，也没有研究其表达谱的特征。为了鉴定毛竹的 DOG 基因成员（PeDoG），并研究其家族结构特征和组织表达谱特征，进行了一项研究。基于全基因组和差异转录组数据，在本研究中，我们详细研究了毛竹 PeDoG1 家族的理化性质、基因结构、顺式作用元件、系统发育关系、保守结构（CS）域、CS 基序和表达模式。
发现毛竹的 DOG 家族基因分布在 16 条染色体支架上，有 24 个成员。所有成员都携带 DOG1 结构域，而 23 个成员还携带碱性亮氨酸拉链（bZIP）结构域。根据系统发育关系，我们可以将 PeDoG 基因分为三个亚家族。共方差分析表明，串联重复是 PeDoG 基因扩增的主要驱动力。这些基因上游启动子包含多个顺式作用元件，表明它们可能参与非生物胁迫和激素诱导。根据转录组数据的基因表达模式显示，PeDoG 基因参与组织和器官发育。使用短时间序列表达挖掘器（STEM）工具进行分析表明，PeDoG 基因家族也与快速早期芽生长有关。基因本体论（GO）和 KEGG 分析表明，PeDoG 基因具有双重作用。我们发现 PeDoGs 通过调节 Polar like1（PL1）基因的表达，作为 bZIP 转录因子发挥作用，从而在毛竹中发挥疾病反应作用。PeDoG 基因的定量基因表达表明，它们在根和叶中大量表达，并能响应赤霉素（GA）诱导表达。
在这项研究中，我们发现 PeDoG 基因参与了广泛的活动，如生长和发育、应激反应和转录。这是首次报道 PeDoG 基因及其在毛竹中的潜在作用。
