Full-Length Transcriptome Assembly of Platycladus orientalis Root Integrated with RNA-Seq to Identify Genes in Response to Root Pruning

Abstract

Platycladus orientalis (P. orientalis) is a common tree used for vegetation restoration in northern China, and its large area propagation helps to improve site conditions. However, under harsh conditions such as poor land, the survival rate of P. orientalis is very low. Numerous studies have shown that root pruning can promote the formation of lateral roots in seedlings, enhancing the roots’ capacity to absorb soil nutrients and water, and thereby improving the survival rate of seedlings. In this study, a one-third root pruning treatment was applied to P. orientalis seedlings, and the whole transcriptome of seedlings subjected to both control (CK) and root pruning treatments was sequenced to analyze their gene expression profiles. This study investigated the regulatory mechanisms of lateral root development in response to root pruning damage at the molecular level. Using nine cells, 15.28 Gb of clean data were obtained, which yielded 101,688 high-quality full-length transcript sequences and 22,955 low-quality full-length transcript sequences after clustering. Redundancy was then removed using CD-HIT, and Illumina RNA-seq sequencing produced 139.26 Gb of clean data. A total of 2025 differentially expressed genes (DEGs) were identified at three time points following root pruning treatment. Enrichment analysis revealed that the peroxidase gene family plays a significant role in lateral root proliferation. Furthermore, the expression levels of the peroxidase gene family were notably upregulated in comparison to the control group. Pathway enrichment analysis identified 22 relevant genes, which appeared to be highly associated with root growth and resilience to stress. Through examining the expression patterns and correlations of these genes, five central genes emerged as key players. The findings of this research suggest that the peroxidase gene family plays a crucial role in the stress response and root development of P. orientalis, providing reference and guidance for root development in other plant species.