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. 2021 Jul 2;22(1):494.
doi: 10.1186/s12864-021-07777-x.

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Mary Luz Yaya Lancheros  1 , Krishan Mohan Rai  2   3 , Vimal Kumar Balasubramanian  2   4 , Lavanya Dampanaboina  2 , Venugopal Mendu  2 , Wilson Terán  5
Affiliations

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Mary Luz Yaya Lancheros et al. BMC Genomics. .

Abstract

Background: Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees.

Results: For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR.

Conclusions: We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

Keywords: Differential gene expression; RNA-seq; Wood development; Xylem.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Main GO categories assigned to xylem reference transcriptome of G. arborea
Fig. 2
Fig. 2
Main families of transcription factors identified in the xylem transcriptome. Blue bars indicate the number of transcripts belonging to each family
Fig. 3
Fig. 3
Phylogenetic analysis of G. arborea NAC transcription factors: VND7, NST1 and SND2 protein sequences identified from the reference transcriptome of G. arborea (Ga) were compared to homologs from other species: At: Arabidopsis thaliana (Q9C8W9, Q84WP6, O49459), Bd: Brachypodium distachyum (Bradi1g04150.1.p, Bradi1g06970.1.p, Bradi1g37898.1.p), Cp: Carica papaya (XP_021889039), Gm: Glycine max (XP_006589457.1, Glyma.01G046800.1.p, Glyma.01G005500.1.p), Nt: Nicotiana tabacum (XP_016440678.1), Pa: Picea abis (MA_101849g0010), Pt: Populus trichocarpa (XP_024447115.1, Potri.001G061200.1, Potri.001G343800.1), Si: Sesamum indicum (XP_011096365), Sly: Solanum lycopersicum (Solyc01g009860.2.1, Solyc01g102740.2.1), Vv: Vitis vinifera (GSVIVT01000940001, XP_002267383, GSVIVT01015274001). The clustering method used for dendrogram construction was neighbor-joining. Line length indicates the evolutionary distance. Uniprot, NCBI protein, TAIR and PlantTFDB accession IDs are shown in parenthesis. In the case of Picea abis, accession was obtained from iTAK plant transcription factor database
Fig. 4
Fig. 4
Distribution of differentially expressed transcripts (DEG) with a p-value < 0.05. DEG are shown in red and the non-DEG are shown in black
Fig. 5
Fig. 5
Differential expression between leaf and stem according to the main metabolic processes in which they are involved. The logarithm of changes of expression for each transcript is represented in red color (induction in stem, Log2FC ≥ 2) and blue (repression in xylem, induction in leaf, Log2FC ≤ -2). Analysis was performed using the MapMan visualization software [93]
Fig. 6
Fig. 6
Differential expression of genes of the monolignol pathway, according to the logarithm of fold change (Log2FC). Transcripts corresponding to each gene are represented in squares. In red are represented the Log2FC values ≥2 (induction in xylem) and in blue the Log2FC values ≤-2 (repressed in xylem). Pathway analysis was performed using the MapMan visualization software [93]
Fig. 7
Fig. 7
Differential expression of transcript isoforms encoding transcription factors involved in the regulation of the monolignol pathway. Red color represents Log2FC values ≥2 (induction in xylem) and blue color Log2FC values ≤-2 (repressed in xylem, induction in leaf)
Fig. 8
Fig. 8
Genes related to the synthesis of other elements of the secondary cell wall with differential gene expression between stem and leaf. Red color represents Log2FC values ≥2 (induction in xylem), blue colors Log2FC values ≤ - 2 (repressed in xylem). Log2FC values of all transcript isoforms of the same gene are presented
Fig. 9
Fig. 9
Phylogenetic analysis of G. arborea PAL (A) and CAD (B) proteins. Protein sequences of PAL and CAD enzymes obtained from G. arborea full length cognate transcripts were compared to homologous sequences belonging to other plant species. Dendrograms were constructed using the neighbor-joining clustering method. Line length indicates the evolutionary distance. In addition to G. arborea (Ga) putative PAL1 sequence, other protein sequences used in PAL phylogenetic analysis were: Ath: Arabidopsis thaliana, with four paralogs of PAL included in the analysis, AthPAL1 (P35510), AthPAL2 (OAP06573), AthPAL3 (OAO94639) and AthPAL4 (OAP02490.1). Car: Coffea arabica (AEL21616), Lca: Lonicera caerulea (ALU09327), Nta: Nicotiana tabacum (NP_001312352.1), Min: Mangifera indica (AIY24975.1), Mof: Melissa officinalis (CBJ23826.1), Pfr: Perilla frutescens (AEZ67457.1), Psc: Plectranthus scutellarioides (AFZ94859.1), Pca: Pogostemon cablin (AJO53272.1), Ptri: Populus trichocarpa (P45730), Rco: Ricinus communis (AGY49231.1), Smi: Salvia miltiorrhiza (ABD73282), Sba: Scutellaria baicalensis (ADN32766.1), Sin: Sesamum indicum (XP_011094662), Vvi: Vitis vinifera (ABM67591), Protein sequences used in CAD phylogenetic analysis, included two possible variants of Gmelina arborea (Ga), the first one induced in stem (CADS, putative CAD3) and the second one induced in leaves (CADL). Other CAD protein sequences used were: Ath: Arabidopsis thaliana CAD1 (OAP16446.1) and CAD2 (NP_179765), Egr: Eucalyptus grandis (XP_010024064.1), Jcu: Jatropha curcas (XP_012086572.1), Jre: Juglans regia (XP_018827699.1), Lp: Lolium perenne (AAB70908), Ote: Ocimum tenuiflorum (ADO16245.1), Os: Oryza sativa (Q6ZHS4), Pni: Populus nigra (AFR37935.1), Pto: Populus tomentosa (AAR83343.1), Rs: Rauvolfia serpentine (ALW82980.1), Sm: Salvia miltiorrhiza (ADN78309.1), Sin: Sesamum indicum (XP_011097452.1), She: Sinopodophyllum hexandrum (AEA36767.1), Tgr: Tectona grandis (ANG60951.1, ANG60952.1, ANG60953.1, ANG60954.1), Vvi: Vitis vinifera (RVW57228.1), Zm: Zea mays (NP_001105654). Different CAD members were included for some species. Accession IDs from protein NCBI database are shown in parenthesis
Fig. 10
Fig. 10
RT-qPCR differential expression validation of a selection of seven G. arborea genes. Bars indicate log2FC of xylem expression compared with leaf expression: black bars, mean log2FC values obtained from RT-qPCR assays; gray bars, mean log2FC values obtained from RNA-seq data
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