The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling

Abstract

Summary Chinese fir (Cunninghamia lanceolata), a commercially important tree for the timber and pulp industry, is widely distributed in southern China and northern Vietnam, but its large and complex genome has hindered the development of genomic resources. Few efforts have focused on analysis of the modulation of transcriptional networks in vascular cambium during the transition from active growth to dormancy in conifers. Here, we used Illumina sequencing to analyze the global transcriptome alterations at the different stages of vascular cambium development in Chinese fir. By analyzing dynamic changes in the transcriptome of vascular cambium based on our RNA sequencing (RNA‐Seq) data at the dormant, reactivating and active stages, many potentially interesting genes were identified that encoded putative regulators of cambial activity, cell division, cell expansion and cell wall biosynthesis and modification. In particular, the genes involved in transcriptional regulation and hormone signaling were highlighted to reveal their biological importance in the cambium development and wood formation. Our results reveal the dynamics of transcriptional networks and identify potential key components in the regulation of vascular cambium development in Chinese fir, which will contribute to the in‐depth study of cambial differentiation and wood‐forming candidate genes in conifers.

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

“…In the cellular component category, 41 6.66%) represent the most abundant sub-categories. These GO classification results are similar to those revealed in previous transcriptomic studies of Chinese fir [23,43]. GO annotations describe the contour features of the overall gene expression of Chinese fir among root, stem, and leaf tissues, and revealed expressed genes encoding inorganic phosphate transporter activity functions like transporter activity-the primary focus of this study.…”

“…GO annotations describe the contour features of the overall gene expression of Chinese fir among root, stem, and leaf tissues, and revealed expressed genes encoding inorganic phosphate transporter activity functions like transporter activity-the primary focus of this study. classification results are similar to those revealed in previous transcriptomic studies of Chinese fir [23,43]. GO annotations describe the contour features of the overall gene expression of Chinese fir among root, stem, and leaf tissues, and revealed expressed genes encoding inorganic phosphate transporter activity functions like transporter activity-the primary focus of this study.…”

“…Due to a lack of homologous unigenes, the average length of unigenes for non-model plants is usually less than 500 bp [26,44,45]. Surprisingly, the unigenes we assembled revealed a mean length of 520 bp, which is longer than those achieved in previous studies of Chinese fir as reported by Huang et al [43]. However, the length distribution of the unigenes was similar to that of the transcripts, and 75.18% unigenes were less than 500 bp, indicating that the length distribution of the transcripts and unigenes was mainly represented by short sequences with relatively little redundancy.…”

“…However, the quality of the data may be affected by several factors, including the contamination of adapter sequences, poor quality reads, and assembly errors [23]. In this study, a total of 236,529,278 clean reads and 35.47 Gbs of databases were obtained from Chinese fir transcriptomes, which is much more than any previously published transcriptome research on Chinese fir [23][24][25]43]. Due to a lack of homologous unigenes, the average length of unigenes for non-model plants is usually less than 500 bp [26,44,45].…”

De novo assembly and characterization of stress transcriptome and regulatory networks under temperature, salt and hormone stresses in Lilium lancifolium

“…Illumina paired-end sequencing, assembly, and functional annotation It is the fact that the RNA-Seq approach has the potential to supersede microarrays due to their higher sensitivity and greater dynamic range of the gene expression [27]. In our search, we obtained 37,843 unigenes, and 18,736 (49.50 %) annotating in the SP library using the Illumina paired-end sequencing technology (Table 1).…”