Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

BMC Genomics
Melissa M L WongRatnam Wickneswari

Abstract

Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identifi...Continue Reading

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Datasets Mentioned

BETA
SRR098315
SRR098314
AAW78382.1
AAY86361.1
ABD42947.1
ABX75853.1
and
ABX75854.1
CAE09058.1
AAQ62540.1

Methods Mentioned

BETA
RNA-seq
EST sequencing
PCR
genotyping
electrophoresis

Software Mentioned

ExPASy Translate Tool
Bioedit ClustalW
MUMMER
miRbase
Blastp
Python script
MEGA
FrameDP
PlnTFDB
Python scripts

Related Concepts