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

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.

De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development

“…After quality control and assembly evaluation, a total of 47.83 GB of high-quality cleaning data and 49,716 unigenes were obtained, with an average length of 1124.51 bp and N50 of 1928 bp. These length attributes of unigenes had better performance than the published data of Camellia Sasanqua [ 30 ], Rhododendron Rex [ 31 ], Ocimum Americanum [ 32 ] and Gmelina area [ 33 ], and the good quality of this transcriptome data was available for the subsequent analysis.…”

ENFOQUES GENÓMICOS Y TRANSCRIPTÓMICOS PARA ESTUDIAR ÁRBOLES MADERABLES: PERSPECTIVAS PARA EL ESTUDIO DE CEDRO ROJO (Cedrela odorata L.)

“…Las tecnologías de secuenciación masiva han aumentado su disponibilidad y con esto se han disminuido costos, lo cual ha permitido un gran avance en la forma en la que se estudian diversas áreas, como por ejemplo los árboles maderables. Gracias a estas tecnologías se han logrado secuenciar genomas completos, para conocer los genes presentes en árboles maderables, lo cual ha permitido un entendimiento en su biología y genética, también se han identificado variaciones genéticas responsables de rasgos específicos de la madera como contenido de lignina y densidad, así como genes relacionados con la resistencia a enfermedades, calidad de madera, adaptación de maderables a diferentes climas, se ha podido evaluar también la respuesta de los maderables a diversos factores ambientales, lo cual está relacionado con la selección y mejora de maderables (Slatko et al, 2018;Ouyng., et al 2016;Yaya Lancheros et al, 2021;Yasodha et al, 2018).…”