De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism
Abstract
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. 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 leavesmore »
- Authors:
-
[1]
- Pontifica Universidad Catolica de Chile, Bogotá (Colombia). Dept. of Biology
- Texas Tech Univ., Lubbock, TX (United States). Dept. of Plant and Soil Sciences, Fiber and Biopolymer Research Inst.; Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Plant and Microbial Biology
- Texas Tech Univ., Lubbock, TX (United States). Dept. of Plant and Soil Sciences, Fiber and Biopolymer Research Inst.; Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Texas Tech Univ., Lubbock, TX (United States). Dept. of Plant and Soil Sciences, Fiber and Biopolymer Research Inst.
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1815703
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 22; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; RNA-seq; Xylem; Differential gene expression; Wood development
Citation Formats
Yaya Lancheros, Mary Luz, Rai, Krishan Mohan, Balasubramanian, Vimal Kumar, Dampanaboina, Lavanya, Mendu, Venugopal, and Terán, Wilson. De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism. United States: N. p., 2021.
Web. doi:10.1186/s12864-021-07777-x.
Yaya Lancheros, Mary Luz, Rai, Krishan Mohan, Balasubramanian, Vimal Kumar, Dampanaboina, Lavanya, Mendu, Venugopal, & Terán, Wilson. De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism. United States. https://doi.org/10.1186/s12864-021-07777-x
Yaya Lancheros, Mary Luz, Rai, Krishan Mohan, Balasubramanian, Vimal Kumar, Dampanaboina, Lavanya, Mendu, Venugopal, and Terán, Wilson. Fri .
"De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism". United States. https://doi.org/10.1186/s12864-021-07777-x. https://www.osti.gov/servlets/purl/1815703.
@article{osti_1815703,
title = {De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism},
author = {Yaya Lancheros, Mary Luz and Rai, Krishan Mohan and Balasubramanian, Vimal Kumar and Dampanaboina, Lavanya and Mendu, Venugopal and Terán, Wilson},
abstractNote = {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. 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. 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.},
doi = {10.1186/s12864-021-07777-x},
journal = {BMC Genomics},
number = 1,
volume = 22,
place = {United States},
year = {Fri Jul 02 00:00:00 EDT 2021},
month = {Fri Jul 02 00:00:00 EDT 2021}
}
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