Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Abstract

Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties from those of normal wood (NW). Chinese fir (Cunninghamia lanceolata) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253 de-novo full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.

Seasonal Developing Xylem Transcriptome Analysis of Pinus densiflora Unveils Novel Insights for Compression Wood Formation

“…The activities of these genes predominantly increased during the SP and decreased in FA. In the context of previous research, it was noted that CW had an increase in not only lignin-related genes (such as PAL, C3H, 4CL, CAD, HCT, and CCoAOMT) but also those related to cellulose biosynthesis (such as CSLA) [ 21 , 24 ]. In contrast, our study observed no abundant expression in CW of these genes, with the exception of laccase ( Figure 5 and Figure 6 ).…”

“…Gymnosperm wood is characterized by high lignin content (25–35%), an HG-type of lignin with more guaiacyl (G) units but a small portion of p-hydroxyphenyl (H) units., whereas angiosperm wood has a lignin content of 15–28%, with a GS-lignin having different proportions of syringyl (S) units [ 22 , 23 ]. It has recently been shown that laccase, responsible for monolignol polymerization, is crucial for lignin biosynthesis in compression wood [ 22 , 24 ]. Lignin-derived fuels have gained popularity in recent years as a technology to produce biofuels from biomass with the potential to reduce dependence on fossil fuels and greenhouse gas emissions [ 25 ].…”

Are TaNAC Transcription Factors Involved in Promoting Wheat Yield by cis-Regulation of TaCKX Gene Family?

“…Among the several TaNAC TFs that bind to the selected TaCKX GFM cis-regulatory sequences, we selected only one TaNAC TF with the highest binding affinity parameters for each selected TaCKX GFM, except TaCKX10-7B (Table 1), for further characterization. Similarly to us, in several studies, including Pompili [35][36][37], other authors have used the plant transcription factor database (PlantTFDB v5.0) to identify transcription factors. The names of the selected TaNAC TFs in the NCBI database were identified as: transcription factor JUNGBRUNNEN 1-like, NAC domain-containing protein 13-like, putative NAC domain-containing protein 94, and protein BEARSKIN-1-like, which bind to the cis-regulatory sites of the TaCKX1-3A, TaCKX2.2.1-3B, TaCKX5-3D, TaCKX9-1B, and TaCKX10-7B TaCKX GFMs, respectively.…”

Transcriptome Profiling of Stem-Differentiating Xylem in Response to Abiotic Stresses Based on Hybrid Sequencing in Cunninghamia lanceolata

“…Our previous study showed that MYB2, MYB21, and MYB092 are differentially expressed upon compression stress in Cunninghamia lanceolata (Lamb.) Hook (C. lanceolata) [43]. C. lanceolata, as endemic and evergreen coniferous species, is one of the most important artificial timber forest species in southern China because of its high timber quality and fast growth [43,44].…”

“…Hook (C. lanceolata) [43]. C. lanceolata, as endemic and evergreen coniferous species, is one of the most important artificial timber forest species in southern China because of its high timber quality and fast growth [43,44]. C. lanceolata is gradually suffering from increased stress, including temperature [45], drought stress [46], and autotoxicity caused by allelopathic toxins such as phenolic acids [47].…”