College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
BMC Genomics. 2024 Feb 14;25(1):179. doi: 10.1186/s12864-024-10091-x.
Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed.
Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments.
In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration.
基因表达模式与生物表型相关，广泛用于探索基因功能。其进化对于理解物种形成和分化也至关重要。棉属是研究植物进化和多倍体化的典型模式生物。然而，棉花物种分化过程中基因表达的进化仍未得到广泛讨论。
基于幼苗叶片转录组，本研究分析了包括六个二倍体和两个天然四倍体在内的八个棉花物种的转录组内容和表达模式。研究结果表明，尽管这些棉花转录组的生物学功能基本保持保守，但在物种分化过程中，转录组内容发生了显著变化。此外，我们对棉花物种间的表达距离进行了全面分析。这一分析进一步支持将 G. arboreum 用作天然棉花多倍体 A 基因组供体的替代。此外，我们的研究强调了应激响应途径的进化，包括激素信号转导、脂肪酸降解和类黄酮生物合成。这些过程似乎在较低的选择压力下进化，可能反映了它们在研究棉属物种适应不同环境中的关键作用。
综上所述，本研究深入了解了棉属内基因表达的变化，并确定了与棉花物种进化密切相关的关键基因/途径。此外，描述在意外高或低选择压力下的基因和途径的方法也可以作为探索基因功能的新策略。
