Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
Int J Mol Sci. 2022 Oct 14;23(20):12297. doi: 10.3390/ijms232012297.
Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways.
随着气候变化，全球范围内严重的干旱条件和极端天气事件日益增多，威胁着本地植物群落和生态系统的持续存在。许多研究已经调查了植物对干旱响应的基因组基础。然而，这项研究在植物界的广泛程度尚不清楚，特别是在对自然生态系统可持续性至关重要的物种中。本研究旨在扩大我们对受干旱胁迫植物中从基因组到表型（G2P）连接的理解，并确定未来研究的重点分类群。开发了生物信息学管道，从数据库中挖掘和链接信息，并从 7730 篇出版物中提取摘要。这种方法确定了 497 个植物分类群中与干旱响应相关的 1634 个基因。这些物种中的大多数（83.30%）已被人类使用分类，并且大多数 G2P 相互作用已在模式生物或作物物种中进行了描述。我们的分析确定了 G2P 研究文献和数据库连接中的几个空白，NCBI 中只有 21%的摘要与基因和分类学数据相关联。摘要文本挖掘在识别潜在的 G2P 途径方面更为成功，有 34%的摘要包含基因、分类群和表型信息。将 G2P 研究扩展到包括非模式植物，特别是那些适应干旱胁迫的植物，将有助于我们深入了解干旱响应的 G2P 途径。
