Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight Into Molecular Mechanisms of Cellulose and Lignin Biosynthesis in Cunninghamia lanceolata

Abstract

Cunninghamia lanceolata is an essential timber species that provide 20%–30% raw materials for China’s timber industry. Although a few transcriptomes have been published in C. lanceolata, full-length mRNA transcripts and regulatory mechanisms behind the cellulose and lignin biosynthesis have not been thoroughly investigated. Here, PacBio Iso-seq and RNA-seq analyses were adapted to identify the full-length and differentially expressed transcripts along a developmental gradient from apex to base of C. lanceolata shoots. A total of 48,846 high-quality full-length transcripts were obtained, of which 88.0% are completed transcriptome based on benchmarking universal single-copy orthologs (BUSCO) assessment. Along stem developmental gradient, 18,714 differentially expressed genes (DEGs) were detected. Further, 28 and 125 DEGs were identified as enzyme-coding genes of cellulose and lignin biosynthesis, respectively. Moreover, 57 transcription factors (TFs), including MYB and NAC, were identified to be involved in the regulatory network of cellulose and lignin biosynthesis through weighted gene co-expression network analysis (WGCNA). These TFs are composed of a comparable regulatory network of secondary cell wall formation in angiosperms, revealing a similar mechanism may exist in gymnosperms. Further, through qRT-PCR, we also investigated eight specific TFs involved in compression wood formation. Our findings provide a comprehensive and valuable source for molecular genetics breeding of C. lanceolata and will be beneficial for molecular-assisted selection.

Crop Improvement by Omics and Bioinformatics

“…In rice, Sun et al found that DROT1 can improve drought tolerance, mainly by regulating the cell wall fiber content and crystal structure in microtubule tissues to enhance drought resistance (Sun et al, 2022). Du et al found that TaERF87 (ethylene response factor (ERF)) could interact with TaAKS1 to enhance the expression of TaP5CS1 and TaP5CR1, thus improving proline synthesis and drought resistance in wheat (Du et al, 2022). Through a GWAS in maize, it was found that three SNP mutations in ZmSRO1d significantly increased the reactive oxygen species (ROS) content of guard cells, promoted stomatal closure, enhanced drought resistance, and increased the yield of overexpressed ZMSRO1D-R by 60% compared with that in the control .…”

SCL14 Inhibits the Functions of the NAC043–MYB61 Signaling Cascade to Reduce the Lignin Content in Autotetraploid Populus hopeiensis

“…The lignin biosynthesis pathway is a complex process involving many biological events that are strictly regulated by various genes [ 19 ]. Lignin monomer synthase genes, including PAL , 4CL , COMT , HCT , CSE , CCR , CAD , and POD , have been investigated in Arabidopsis thaliana [ 20 , 21 ], Populus [ 22 ], and Cunninghamia lanceolata [ 23 ]. PAL is the first enzyme-encoding gene involved at the beginning of this pathway, and it determines the metabolic flow of the entire pathway [ 24 ].…”

Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations

“…Using poly-T oligo-attached magnetic beads, mRNA was extracted from total RNA. cDNA synthesis was implemented following our previous research (Hu et al, 2022). RNA sequencing was implemented by using Illumina NovaSeq 6,000 platform and 150 bp paired-end raw reads were generated.…”

“…qRT-PCR was implemented with the TB Green Premix Ex Taq II (Tli RNaseH Plus; Takara) on CFX96 real-time PCR detection system (CFX96; Bio-Rad, United States). The expression pattern was assessed by our previous protocol (Hu et al, 2022). For each gene and sample, the qRT-PCR data were acquired from three biological and three technical repeats.…”