Kościelniak Paulina, Walas Łukasz, Konecka Agata, Buraczyk Włodzimierz, Klupczyńska Ewelina A
Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61614, Poznań, Poland.
Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62030, Kórnik, Poland.
Biol Res. 2025 Jun 10;58(1):37. doi: 10.1186/s40659-025-00610-9.
Analysis of plant and animal genomes is essential for understanding their biological function, adaptation, and evolution. Human genomic databases are the most advanced due to extensive research on the genetic basis of disease and personalized medicine. Key resources include GenBank, Ensembl, the 1000 Genomes Project, and GTEx, which provide detailed information on genome sequences, genetic variation, and gene expression in different tissues. Similarly, genomic and transcriptome databases for animals are relatively well-developed, particularly for model organisms such as Mus musculus, Drosophila melanogaster, and Danio rerio. In contrast, plant genomic databases are developing rapidly but remain less comprehensive than those for humans and animals. This discrepancy is primarily due to the high species diversity and complexity of plant genomes, which are often characterized by gene duplication and significant structural variability. Databases such as Phytozome, TAIR (The Arabidopsis Information Resource), Gramene, and Planteome focus mainly on model plants and agriculturally important species. Another crucial factor is the lower funding for plant-related projects, despite the substantial investment required due to the large size and complexity of plant genomes. This disparity is also evident in the study of long non-coding RNAs (lncRNAs), which play a key role in the growth and development of organisms. In plants, genome complexity-driven by factors such as considerable length, polyploidy, and epigenetic modifications-poses significant challenges for research. Despite these obstacles, understanding lncRNAs in plants, particularly in forest trees, is of paramount importance. lncRNAs hold great potential for applications in agriculture and forestry, especially in the context of climate change. For example, they could enhance our ability to develop resilient tree species capable of withstanding environmental stressors. To achieve this, a comprehensive understanding of lncRNA functions at the molecular and biological levels, as well as the development of robust and complete databases, is urgently needed. In the near future, computational analyses are expected to play a key role in overcoming these challenges. In this article, we review the current state of knowledge about lncRNAs in plants, highlight the obstacles to their study, and explore how advances in this field could revolutionize agriculture and forestry. By focusing on the unique challenges and opportunities presented by forest trees, we emphasize the crucial role of lncRNA research in addressing global environmental challenges.
分析植物和动物基因组对于理解它们的生物学功能、适应性和进化至关重要。由于对疾病的遗传基础和个性化医疗进行了广泛研究，人类基因组数据库最为先进。关键资源包括GenBank、Ensembl、千人基因组计划和GTEx，它们提供了不同组织中基因组序列、遗传变异和基因表达的详细信息。同样，动物的基因组和转录组数据库也相对发达，特别是对于小家鼠、黑腹果蝇和斑马鱼等模式生物。相比之下，植物基因组数据库正在迅速发展，但仍不如人类和动物的数据库全面。这种差异主要是由于植物基因组的物种多样性高和复杂性，其特点通常是基因重复和显著的结构变异性。Phytozome、TAIR（拟南芥信息资源）、Gramene和Planteome等数据库主要关注模式植物和具有农业重要性的物种。另一个关键因素是与植物相关项目的资金投入较低，尽管由于植物基因组的规模大且复杂需要大量投资。这种差距在长链非编码RNA（lncRNA）的研究中也很明显，lncRNA在生物体的生长和发育中起关键作用。在植物中，由相当长的长度、多倍体和表观遗传修饰等因素驱动的基因组复杂性给研究带来了重大挑战。尽管存在这些障碍，但了解植物中的lncRNA，特别是在林木中的lncRNA，至关重要。lncRNA在农业和林业中具有巨大的应用潜力，特别是在气候变化的背景下。例如，它们可以增强我们培育能够抵御环境压力的有韧性树种的能力。为了实现这一目标，迫切需要在分子和生物学水平上全面了解lncRNA的功能，以及开发强大而完整的数据库。在不久的将来，计算分析有望在克服这些挑战中发挥关键作用。在本文中，我们回顾了植物lncRNA的当前知识状态；突出了它们研究中的障碍；并探讨了该领域的进展如何能够彻底改变农业和林业。通过关注林木带来的独特挑战和机遇，我们强调了lncRNA研究在应对全球环境挑战中的关键作用。
