Development from single cells to multicellular tissues and organs involves more than just the exact replication of cells, which is known as differentiation. The primary focus of research into the mechanism of differentiation has been differences in gene expression profiles between individual cells. However, it has predominantly been conducted at low throughput and bulk levels, challenging the efforts to understand molecular mechanisms of differentiation during the developmental process in animals and humans. During the last decades, rapid methodological advancements in genomics facilitated the ability to study developmental processes at a genome-wide level and finer resolution. Particularly, sequencing transcriptomes at single-cell resolution, enabled by single-cell RNA-sequencing (scRNA-seq), was a breath-taking innovation, allowing scientists to gain a better understanding of differentiation and cell lineage during the developmental process. However, single-cell isolation during scRNA-seq results in the loss of the spatial information of individual cells and consequently limits our understanding of the specific functions of the cells performed by different spatial regions of tissues or organs. This greatly encourages the emergence of the spatial transcriptomic discipline and tools. Here, we summarize the recent application of scRNA-seq and spatial transcriptomic tools for developmental biology. We also discuss the limitations of current spatial transcriptomic tools and approaches, as well as possible solutions and future prospects.

Investigating the spatial distributions and associations of tree populations provides better insights into the dynamics and processes that shape the forest community. Korean pine (Pinus koraiensis) is one of the most important tree species in broad-leaved Korean pine mixed forests (BKMFs), and little is known about the spatial point patterns of and associations between Korean pine and community-level woody species groups such as coniferous and deciduous trees in different developmental stages. This study investigated the spatial patterns of Korean pine (KP) trees and then analyzed how the spatial associations between KP trees and other tree species at the community level vary in different BKMFs. Extensive data collected from five relatively large sample plots, covering a substantial area within the natural distribution range of KP in northeastern China, were utilized. Uni- and bivariate pair correlation functions and mark correlation functions were applied to analyze spatial distribution patterns and spatial associations. The DBH (diameter at breast height) histogram of KP trees in northeastern China revealed that the regeneration process was very poor in the Changbai Mountain (CBS) plot, while the other four plots exhibited moderate or expanding population structures. KP trees were significantly aggregated at scales up to 10 m under the HPP null model, and the aggregation scales decreased with the increase in size classes. Positive or negative spatial associations were observed among different life stages of KP trees in different plots. The life history stages of the coniferous tree group showed positive spatial associations with KP saplings and juvenile trees at small scales, and spatial independence or negative correlations with larger KP trees at greater scales. All broad-leaved tree groups (canopy, middle, and understory layers) exhibited only slightly positive associations with KP trees at small scales, and dominant negative associations were observed at most scales. Our results demonstrate that mature KP trees have strong importance in the spatial patterns of KP populations, and site heterogeneity, limited seed dispersal, and interspecific competition characterize the spatial patterns of KP trees and community-level spatial associations with respect to KP trees, which can serve as a theoretical basis for the management and restoration of BKMFs in northeastern China.