Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid

S. Y C Yong, Chee Yen Choong, P. L. Cheong, S. L. Pang, R. Nor Amalina, J. A. Harikrishna, M. N. Mat-Isa, P. Hedley, L. Milne, R. Vaillancourt, R Wickneswari V Ratnam

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

The majority of plant expressed sequence tags (ESTs) available in the public databases are from non-woody species such as Arabidopsis, maize, soybean, and rice, with the exception of the model tree species, Populus. In this study, we report the first EST database constructed from the commercially important tree species Acacia. ESTs were generated from pooled RNA extracted from the mature, intermediate, and young inner bark tissues of an Acacia auriculiformis x Acacia mangium hybrid. Finally, 3,182 high-quality ESTs were analyzed representing a total of 1,982 unique transcripts (663 contigs and 1,319 singletons) for the inner bark cDNA library. A total of 1,053 unigenes (1,750 ESTs) showed similarities with protein sequences in public database where 867 were significant matches (E value ≤ e-10). Further analysis performed on unigenes with significant matches and known functions identified 231 genes including genes involved in cellulose, lignin, and hemicellulose biosynthesis. For cDNA library validation, quantitative real-time RT-PCR was performed to study the expression levels of the cellulose and lignin genes identified from this EST database in the phloem tissue of A. mangium, A. auriculiformis, and A. auriculiformis x A. mangium hybrid. All the seven candidate genes were expressed in all the individuals studied confirming the dependability of the EST database. The cDNA library and the EST database constructed are valuable resources for forest tree research aiming towards understanding the genetic control of wood formation and in the future endeavors to modify wood and fiber profile through marker-assisted breeding programs.

Original languageEnglish
Pages (from-to)143-152
Number of pages10
JournalTree Genetics and Genomes
Volume7
Issue number1
DOIs
Publication statusPublished - 2011

Fingerprint

Acacia auriculiformis
Acacia
Acacia mangium
Expressed Sequence Tags
expressed sequence tags
bark
Databases
gene
Gene Library
cDNA libraries
unigenes
lignin
cellulose
Lignin
Cellulose
Genes
genes
phloem
Populus
Phloem

Keywords

  • cDNA library
  • Comparative sequence analysis
  • Library validation
  • Transcript profiling
  • Wood formation genes

ASJC Scopus subject areas

  • Forestry
  • Horticulture
  • Genetics
  • Molecular Biology

Cite this

Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid. / Yong, S. Y C; Choong, Chee Yen; Cheong, P. L.; Pang, S. L.; Nor Amalina, R.; Harikrishna, J. A.; Mat-Isa, M. N.; Hedley, P.; Milne, L.; Vaillancourt, R.; V Ratnam, R Wickneswari.

In: Tree Genetics and Genomes, Vol. 7, No. 1, 2011, p. 143-152.

Research output: Contribution to journalArticle

Yong, SYC, Choong, CY, Cheong, PL, Pang, SL, Nor Amalina, R, Harikrishna, JA, Mat-Isa, MN, Hedley, P, Milne, L, Vaillancourt, R & V Ratnam, RW 2011, 'Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid', Tree Genetics and Genomes, vol. 7, no. 1, pp. 143-152. https://doi.org/10.1007/s11295-010-0321-y
Yong, S. Y C ; Choong, Chee Yen ; Cheong, P. L. ; Pang, S. L. ; Nor Amalina, R. ; Harikrishna, J. A. ; Mat-Isa, M. N. ; Hedley, P. ; Milne, L. ; Vaillancourt, R. ; V Ratnam, R Wickneswari. / Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid. In: Tree Genetics and Genomes. 2011 ; Vol. 7, No. 1. pp. 143-152.
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AU - Harikrishna, J. A.

AU - Mat-Isa, M. N.

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AU - Vaillancourt, R.

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