An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium ‘Zhongshanshan’

Abstract

Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

“…However, scarecrow-like protein 6 (TRINITY_DN18674_c0_g2) was upregulated in CK3 vs. TM3 but not differentially expressed at 7 dpt. Auxin-responsive transcription factor SCR has been shown to play roles in the control of cell division, leading to root primordia differentiation and linking auxin-signaling with cell specification and patterning [17,18]. Additionally, scr mutant's growth rate and meristem size were found to be reduced compared to wild-type plants.…”

“…The pair RBR-SCR has been described extensively in root development. The RBR gene is considered a key cell-cycle regulator downstream of the SCR gene [17]. In Arabidopsis, JA regulates organizer cell activity in the root stem cell niche through the RBR-SCR network and stress response protein ERF115.…”

“…Recent transcriptome analysis has correlated hormone signal transduction, carbohydrate and energy metabolisms, protein degradation, and certain transcription factor (TF) activities with AR formation in Taxodium “Zhongshanshan” [ 17 ]. A relationship between adventitious rooting, with or without IBA, and antioxidant enzymes was observed in mung bean seedlings [ 18 ].…”

Peer Review #2 of "Identification and functional analysis of LecRLK genes in Taxodium ‘Zhongshanshan’ (v0.1)"

“…The unigene sequences of Taxodium 'Zhongshanshan' were derived from the previously determined salinity stress transcriptome (Yu et al, 2016), short-term waterlogging transcriptome (Qi et al, 2014), and adventitious roots transcriptome (Wang et al, 2019). Hidden Markov Model (HMM) profiles (PF00069, PF01453, PF00139, PF00059), which correspond to kinase, G-type lectin, L-type lectin, and C-type lectin domains, respectively, were downloaded from the Pfam database (http://pfam.xfam.org/) (El-Gebali et al, 2019).…”

“…Conifers are rarely reported due to the lack of genomic information. With the development of high-throughput sequencing technology, the transcriptome of Taxodium has been published (Qi et al, 2014;Yu et al, 2016;Wang et al, 2019), which has laid a foundation for the identification of large gene families. Here, we conducted a comprehensive bioinformatics analysis of ThzLecRLK gene family based on transcriptome data and analyzed the expression of 15 representative LecRLKs in different tissues and under various stressors.…”